1) 18S amplicons

1.1) Data overview

The dataset “Taraspina 18S miTags” contains reads from 45 samples of Tara Oceans and from 10 samples of Malaspina. On average, each sample contains 4440 OTUs:

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##      93    1840    3086    4440    5808   23780


Overall reads per sample:

1.2) Normalization


In order to keep as many samples as possible, we rarefy at 1154 reads per sample. By that, we loose 10 samples, and after removing the exluded samples in the 16S dataset (to make them comparable), we end up with a normalized dataset containing 43 samples and 5669 OTUs.


Datasets summary:

dim(tb18_tax) #original dataset
## [1] 8642   57
dim(tb18_tax_occur) #original dataset with occurrence data alone
## [1] 8642   55
dim(tb18_tax_occur_min1154) #dataset without samples with less than 1154 OTUs
## [1] 8349   43
dim(tb18_tax_occur_ss1154_no_cero) #rarefied dataset
## [1]   43 5684

1.3) General community analysis

1.3.1) Richness and evenness (Shannon index)

Most of the samples take Shannon Index values around 6:

1.3.2) Richness: OTU number

Lowest number of OTUs per sample:

## [1] 353

Maximum number of OTUs per sample:

## [1] 807

In most of the samples, we can identify between 600 and 700 OTUs:

1.3.3) Index of evenness

1.3.3.1) Pielou’s index

The Pielou index (constrained between 0 and 1) takes values closer to 1 as the variation of species proportion in a sample increases. Most of the samples get values between 0.90 and 0.95, meaning that the numerical composition of different OTUs in a sample is highly variable - there’s no constant presence of dominant species.

1.3.4) Abundance Models

Most of the OTUs show very few occurrences; suggesting that we will probably be able to identify a significant ammount of rare otus:

1.3.4.1) Rank-Abundance or Dominance/Diversity Model (“radfit”)

The OTUs abundance distribution fits relativelly close to log-normal model.

1.3.4.2) Preston’s Log-normal Model

According to Preston’s lognormal model fitted into groups of species’ frequencies, we’re missing 1588.816 species:

## Extrapolated     Observed       Veiled 
##     9937.816     8349.000     1588.816


When computing Prestons’ lognormal model fit without pooling data into groups, we miss 1385.371 species:

## Extrapolated     Observed       Veiled 
##     9734.371     8349.000     1385.371

1.3.5) Rarefaction curves of rarefied and non-rarefied datasets

1.3.6) Beta diversity

1.3.6.1) Dissimilarity matrix using Bray-Curtis index:

The Bray-Curtis dissimilarity, constrained between 0 (minimum distance) and 1 (highest dissimilarity) allows us to quantify the differences between samples according to the composition and the relative abundance of their OTUs. In our dataset, most of the samples pairs take dissimilarity values around 0.8, meaning that their composition is substantially different.

1.3.6.2) Hierarchical clustering

The stations seem to form clusters according to geographic localization, but there are no evident clusters separated from the general groups, apart from the one containing TARA_84, TARA_82 and TARA_85.

(To be done: assign Longhurst provinces information to each station and check if any of the central clusters is meaningful regarding to the samples’ geographical location)

1.3.6.3) Non-metric multidimensional scaling

We can identify a prominent group in the central part of the NMDS plot and a few outliers (TARA 82, 84 and 85) in the central-right edge of the plot. The stress parameter takes a value below 0.2, suggesting that the plot is acceptable.

## 
## Call:
## monoMDS(dist = tb18_tax_occur_ss1154_no_cero.bray) 
## 
## Non-metric Multidimensional Scaling
## 
## 43 points, dissimilarity 'bray', call 'vegdist(x = tb18_tax_occur_ss1154_no_cero, method = "bray")'
## 
## Dimensions: 2 
## Stress:     0.1397828 
## Stress type 1, weak ties
## Scores scaled to unit root mean square, rotated to principal components
## Stopped after 55 iterations: Stress nearly unchanged (ratio > sratmax)

1.4) Geographical analysis

Communities quickly change their composition across geographical distances:

1.4.1) Mantel correlograms

Mantel statistic is -significantlly- so low, meaning that the correlation between samples dissimilarity and geographical distances is weak.

## 
## Mantel statistic based on Pearson's product-moment correlation 
## 
## Call:
## mantel(xdis = geo_distances_MP_18S, ydis = tb18_tax_occur_ss1154_no_cero.bray) 
## 
## Mantel statistic r: 0.1237 
##       Significance: 0.013 
## 
## Upper quantiles of permutations (null model):
##    90%    95%  97.5%    99% 
## 0.0671 0.0866 0.1087 0.1275 
## Permutation: free
## Number of permutations: 999

Correlograms:

MP_18s_ss1154_mantel_correl_by_1000km<-mantel.correlog(tb18_tax_occur_ss1154_no_cero.bray, D.geo=geo_distances_MP_18S, break.pts=seq(0,20000, by=1000))
plot(MP_18s_ss1154_mantel_correl_by_1000km)

MP_18s_ss1154_mantel_correl_by_100km<-mantel.correlog(tb18_tax_occur_ss1154_no_cero.bray, D.geo=geo_distances_MP_18S, break.pts=seq(0,20000, by=100))
plot(MP_18s_ss1154_mantel_correl_by_100km)

1.5) Abundance vs. occurence

OTUs distribution according to their percentage of occurence and relative abundance.
- red line: OTUs that occur in more than 80% of the samples.
- blue line: regionally abundant OTUs (> 0.1%).

Regionally abundant OTUs (relative abundance over 0.1%):

##     otu_names mean_rabund perc_occur                  classif
## 93     OTU_38 0.017451937  90.697674            Pelagophyceae
## 88   OTU_3677 0.014187256  79.069767         Prymnesiophyceae
## 126   OTU_751 0.010640442  39.534884 Prasinophyceae_clade-VII
## 116  OTU_5415 0.010237395  25.581395                     <NA>
## 81   OTU_3374 0.008484140  86.046512            Pelagophyceae
## 50   OTU_2494 0.007113780  72.093023         Prymnesiophyceae
## 55   OTU_2631 0.005783725  72.093023         Prymnesiophyceae
## 76   OTU_3177 0.005763573  46.511628          Mamiellophyceae
## 85   OTU_3569 0.005300069  46.511628          Mamiellophyceae
## 4    OTU_1032 0.005118697  69.767442         Prymnesiophyceae
## 134   OTU_933 0.004796260  95.348837         Prymnesiophyceae
## 80   OTU_3282 0.004735803  46.511628          Mamiellophyceae
## 89   OTU_3729 0.004272299  76.744186            Pelagophyceae
## 115  OTU_5120 0.004111080  39.534884          Mamiellophyceae
## 65   OTU_2910 0.003990166  74.418605                     <NA>
## 104  OTU_4144 0.003949861  46.511628          Mamiellophyceae
## 41   OTU_2200 0.003768490  90.697674                     <NA>
## 83   OTU_3454 0.003587119  76.744186                     <NA>
## 26   OTU_1921 0.003546814  86.046512         Prymnesiophyceae
## 78   OTU_3227 0.003425900  34.883721 Prasinophyceae_clade-VII
## 16   OTU_1597 0.003304986  83.720930         Prymnesiophyceae
## 105  OTU_4176 0.003264681  32.558140          Mamiellophyceae
## 109  OTU_4227 0.003244529  32.558140 Prasinophyceae_clade-VII
## 101  OTU_4123 0.003123615  39.534884 Prasinophyceae_clade-VII
## 72   OTU_3038 0.003103462  81.395349                     <NA>
## 10   OTU_1383 0.003083310  81.395349                     <NA>
## 13   OTU_1456 0.002942243  83.720930              Dinophyceae
## 141   OTU_974 0.002922091  65.116279         Prymnesiophyceae
## 23   OTU_1833 0.002781025  83.720930                     <NA>
## 132   OTU_896 0.002720567  72.093023                     <NA>
## 102  OTU_4125 0.002519044  81.395349            Pelagophyceae
## 99   OTU_4103 0.002418282  39.534884          Mamiellophyceae
## 70   OTU_2996 0.002377978  62.790698                     <NA>
## 30   OTU_2031 0.002337673  62.790698                     <NA>
## 138   OTU_950 0.002216759   4.651163         Prymnesiophyceae
## 79   OTU_3271 0.002196606  30.232558 Prasinophyceae_clade-VII
## 96   OTU_3926 0.002156302  62.790698            Pelagophyceae
## 95   OTU_3871 0.002136149  72.093023                     <NA>
## 103  OTU_4134 0.002075692  53.488372            Pelagophyceae
## 112  OTU_4518 0.002075692  37.209302          Mamiellophyceae
## 137   OTU_949 0.002055540  60.465116         Dictyochophyceae
## 84   OTU_3560 0.001954778  65.116279            Pelagophyceae
## 52   OTU_2553 0.001954778  81.395349                     <NA>
## 131   OTU_893 0.001934626  53.488372                     <NA>
## 45   OTU_2305 0.001874169  72.093023                     <NA>
## 3    OTU_1018 0.001833864  11.627907         Prymnesiophyceae
## 43   OTU_2269 0.001813712  81.395349                     <NA>
## 5    OTU_1047 0.001813712  67.441860                     <NA>
## 62   OTU_2868 0.001813712  53.488372                     <NA>
## 98   OTU_4090 0.001773407  30.232558          Mamiellophyceae
## 53    OTU_256 0.001733102  72.093023                     <NA>
## 125   OTU_717 0.001733102  67.441860              Dinophyceae
## 57   OTU_2654 0.001712950  69.767442            Pelagophyceae
## 108  OTU_4226 0.001712950  41.860465          Mamiellophyceae
## 21   OTU_1746 0.001692798  72.093023         Prymnesiophyceae
## 110  OTU_4260 0.001692798  46.511628          Mamiellophyceae
## 11   OTU_1395 0.001692798  20.930233                     <NA>
## 94    OTU_380 0.001672645  83.720930         Prymnesiophyceae
## 18   OTU_1635 0.001672645  74.418605                     <NA>
## 75   OTU_3124 0.001652493  65.116279                     <NA>
## 9    OTU_1343 0.001632340  69.767442              Dinophyceae
## 31   OTU_2043 0.001612188  60.465116                     <NA>
## 127   OTU_758 0.001612188  60.465116                     <NA>
## 130   OTU_884 0.001531579  81.395349                     <NA>
## 38    OTU_216 0.001531579  62.790698              Dinophyceae
## 140   OTU_973 0.001531579  62.790698                     <NA>
## 117  OTU_5484 0.001511426  34.883721          Mamiellophyceae
## 58   OTU_2686 0.001491274  74.418605                     <NA>
## 19   OTU_1641 0.001491274  72.093023              Dinophyceae
## 40   OTU_2195 0.001491274  72.093023              Dinophyceae
## 64   OTU_2887 0.001491274  69.767442                     <NA>
## 71   OTU_3018 0.001491274  67.441860                     <NA>
## 87    OTU_363 0.001491274  60.465116                     <NA>
## 67   OTU_2965 0.001491274  58.139535                     <NA>
## 113  OTU_4533 0.001450969  44.186047          Mamiellophyceae
## 42   OTU_2207 0.001450969  79.069767              Dinophyceae
## 32   OTU_2078 0.001450969  72.093023                     <NA>
## 51   OTU_2518 0.001410665  55.813953                     <NA>
## 59   OTU_2730 0.001390512  60.465116                     <NA>
## 107  OTU_4203 0.001390512  55.813953            Pelagophyceae
## 133   OTU_914 0.001370360  67.441860         Prymnesiophyceae
## 97   OTU_4089 0.001370360  37.209302          Mamiellophyceae
## 56   OTU_2648 0.001350208  79.069767                     <NA>
## 20   OTU_1694 0.001330055  67.441860                     <NA>
## 74   OTU_3056 0.001330055  65.116279                     <NA>
## 2    OTU_1012 0.001309903  65.116279                     <NA>
## 47   OTU_2429 0.001289751  74.418605         Prymnesiophyceae
## 128   OTU_793 0.001289751  74.418605                     <NA>
## 86   OTU_3602 0.001289751  62.790698                     <NA>
## 54   OTU_2594 0.001289751  58.139535                     <NA>
## 28   OTU_1997 0.001269598  81.395349         Prymnesiophyceae
## 12   OTU_1446 0.001269598  65.116279                     <NA>
## 122  OTU_6181 0.001269598  23.255814                     <NA>
## 123   OTU_628 0.001249446  60.465116              Dinophyceae
## 35   OTU_2120 0.001249446  58.139535                     <NA>
## 139   OTU_952 0.001249446  53.488372              Dinophyceae
## 124  OTU_6608 0.001249446  23.255814                     <NA>
## 119   OTU_584 0.001249446  11.627907                     <NA>
## 27   OTU_1929 0.001229293  44.186047          Mamiellophyceae
## 114   OTU_458 0.001209141  60.465116         Prymnesiophyceae
## 1    OTU_1001 0.001209141  53.488372                     <NA>
## 6    OTU_1066 0.001209141  44.186047         Prymnesiophyceae
## 44   OTU_2284 0.001188989  53.488372                     <NA>
## 73   OTU_3055 0.001188989  53.488372            Chrysophyceae
## 49   OTU_2466 0.001188989  51.162791                     <NA>
## 33   OTU_2086 0.001148684  58.139535              Dinophyceae
## 142   OTU_990 0.001148684  58.139535                     <NA>
## 39   OTU_2189 0.001148684  53.488372                     <NA>
## 82   OTU_3430 0.001148684  30.232558          Mamiellophyceae
## 61   OTU_2853 0.001148684  74.418605         Prymnesiophyceae
## 14   OTU_1496 0.001128532  72.093023                     <NA>
## 111   OTU_437 0.001128532  67.441860         Prymnesiophyceae
## 91   OTU_3751 0.001128532  48.837209                     <NA>
## 15   OTU_1551 0.001108379  67.441860                     <NA>
## 120   OTU_599 0.001108379  65.116279                     <NA>
## 69   OTU_2986 0.001108379  60.465116                     <NA>
## 77   OTU_3196 0.001108379  60.465116         Prymnesiophyceae
## 37   OTU_2158 0.001108379  58.139535         Prymnesiophyceae
## 7    OTU_1087 0.001108379  55.813953                     <NA>
## 135   OTU_936 0.001088227  53.488372                     <NA>
## 129   OTU_825 0.001088227  48.837209                     <NA>
## 66   OTU_2916 0.001088227  46.511628                     <NA>
## 17   OTU_1628 0.001068075  65.116279              Dinophyceae
## 25   OTU_1902 0.001068075  58.139535         Prymnesiophyceae
## 34   OTU_2089 0.001068075  53.488372                     <NA>
## 100  OTU_4115 0.001068075  51.162791                     <NA>
## 60   OTU_2811 0.001047922  46.511628                     <NA>
## 92   OTU_3754 0.001047922  46.511628                     <NA>
## 22   OTU_1825 0.001027770  55.813953                     <NA>
## 90    OTU_373 0.001027770  55.813953                     <NA>
## 63   OTU_2873 0.001027770  53.488372                     <NA>
## 106  OTU_4190 0.001027770  30.232558          Mamiellophyceae
## 118  OTU_5496 0.001027770   9.302326                     <NA>
## 136   OTU_938 0.001007618  65.116279                     <NA>
## 36   OTU_2124 0.001007618  62.790698         Dictyochophyceae
## 8    OTU_1261 0.001007618  60.465116                     <NA>
## 68   OTU_2966 0.001007618  60.465116                     <NA>
## 46   OTU_2365 0.001007618  53.488372                     <NA>
## 48   OTU_2453 0.001007618  53.488372                     <NA>
## 121     OTU_6 0.001007618  44.186047                     <NA>
## 29   OTU_2030 0.001007618  55.813953                     <NA>
## 24   OTU_1879 0.001007618  48.837209         Prymnesiophyceae
##                                                                                                                                                      OTUId
## 93                                    SILVA.v123_KF130487.1.1773_Eukaryota;SAR;Stramenopiles;Ochrophyta;Pelagophyceae;Pelagomonadales;uncultured_eukaryote
## 88                                                       SILVA.v123_X77478.1.1803_Eukaryota;Haptophyta;Prymnesiophyceae;Phaeocystis;Phaeocystis_antarctica
## 126                               SILVA.v123_KJ760716.1.1777_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Clade_VII;Subclade_B;uncultured_eukaryote
## 116                                                     SILVA.v123_AF315604.1.1807_Eukaryota;SAR;Stramenopiles;Bicosoecida;Pseudobodo;Pseudobodo_tremulans
## 81            SILVA.v123_AC236360.17941.19743_Eukaryota;SAR;Stramenopiles;Ochrophyta;Pelagophyceae;Pelagomonadales;Aureococcus;Aureococcus_anophagefferens
## 50                                                  SILVA.v123_KF422607.1.1694_Eukaryota;Haptophyta;Prymnesiophyceae;Phaeocystis;Haptophyceae_sp._CCMP2000
## 55                                                        SILVA.v123_AJ278037.1.1602_Eukaryota;Haptophyta;Prymnesiophyceae;Phaeocystis;Phaeocystis_globosa
## 76  SILVA.v123_FR874477.1.1775_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Bathycoccus;uncultured_marine_picoeukaryote
## 85  SILVA.v123_FR874422.1.1776_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Bathycoccus;uncultured_marine_picoeukaryote
## 4                                                         SILVA.v123_AY851300.1.1802_Eukaryota;Haptophyta;Prymnesiophyceae;Phaeocystis;Phaeocystis_globosa
## 134                                                      SILVA.v123_KJ763007.1.1798_Eukaryota;Haptophyta;Prymnesiophyceae;Phaeocystis;uncultured_eukaryote
## 80         SILVA.v123_AACY020218946.53.1575_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Ostreococcus;marine_metagenome
## 89          SILVA.v123_ACJI01001310.5359.7147_Eukaryota;SAR;Stramenopiles;Ochrophyta;Pelagophyceae;Pelagomonadales;Aureococcus;Aureococcus_anophagefferens
## 115           SILVA.v123_KJ763259.1.1763_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Ostreococcus;uncultured_eukaryote
## 65                                                                                   SILVA.v123_KJ763800.1.1807_Eukaryota;DH147_EKD10;uncultured_eukaryote
## 104 SILVA.v123_FR874693.1.1777_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Bathycoccus;uncultured_marine_picoeukaryote
## 41                                 SILVA.v123_KF130192.1.1763_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_III;uncultured_eukaryote
## 83                                   SILVA.v123_KJ763934.1.1796_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 26                                                   SILVA.v123_HM581633.1.1797_Eukaryota;Haptophyta;Prymnesiophyceae;OLI16010;uncultured_marine_eukaryote
## 78                           SILVA.v123_FJ537298.1.1778_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Clade_VII;Subclade_B;uncultured_Prasinophyceae
## 16                                                          SILVA.v123_KJ762902.1.1800_Eukaryota;Haptophyta;Prymnesiophyceae;OLI16010;uncultured_eukaryote
## 105    SILVA.v123_AF525858.1.1766_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Ostreococcus;uncultured_marine_eukaryote
## 109                          SILVA.v123_FJ537306.1.1756_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Clade_VII;Subclade_B;uncultured_Prasinophyceae
## 101                               SILVA.v123_KF031720.1.1747_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Clade_VII;Subclade_B;uncultured_eukaryote
## 72                                   SILVA.v123_KJ763586.1.1789_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 10                                                                        SILVA.v123_KJ763777.1.1804_Eukaryota;SAR;Alveolata;NIF_4C10;uncultured_eukaryote
## 13                                             SILVA.v123_KJ763154.1.1799_Eukaryota;SAR;Alveolata;Dinoflagellata;Dinophyceae;SCM15C35;uncultured_eukaryote
## 141                                                     SILVA.v123_KF620996.1.1754_Eukaryota;Haptophyta;Prymnesiophyceae;Phaeocystis;uncultured_haptophyte
## 23                                                           SILVA.v123_JQ781940.1.1785_Eukaryota;SAR;Stramenopiles;MAST_1;MAST_1D;uncultured_stramenopile
## 132                                  SILVA.v123_KJ763301.1.1788_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 102             SILVA.v123_JN934690.1.1635_Eukaryota;SAR;Stramenopiles;Ochrophyta;Pelagophyceae;Sarcinochrysidales;Ankylochrisis;Pelagophyceae_sp._RCC2505
## 99           SILVA.v123_AACY023218795.1.1233_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Bathycoccus;marine_metagenome
## 70                                   SILVA.v123_KF130265.1.1745_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 30                                                                      SILVA.v123_KC488619.1.1713_Eukaryota;Incertae_Sedis;Telonema;uncultured_Telonemida
## 138                                     SILVA.v123_KF130149.1.1755_Eukaryota;Haptophyta;Prymnesiophyceae;Prymnesiales;Braarudosphaera;uncultured_eukaryote
## 79                            SILVA.v123_AJ402359.1.1758_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Clade_VII;Subclade_B;eukaryote_clone_OLI11345
## 96                   SILVA.v123_U40257.1.1813_Eukaryota;SAR;Stramenopiles;Ochrophyta;Pelagophyceae;Pelagomonadales;Aureococcus;Aureococcus_anophagefferens
## 95                                  SILVA.v123_KJ760785.1.1797_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 103                SILVA.v123_JQ420078.1.1796_Eukaryota;SAR;Stramenopiles;Ochrophyta;Pelagophyceae;Pelagomonadales;Aureococcus;Aureococcus_anophagefferens
## 112           SILVA.v123_KC583088.1.1775_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Micromonas;uncultured_Chlorophyta
## 137                                                SILVA.v123_KJ759450.1.1797_Eukaryota;SAR;Stramenopiles;Ochrophyta;Dictyochophyceae;uncultured_eukaryote
## 84                                 SILVA.v123_KC488601.1.1695_Eukaryota;SAR;Stramenopiles;Ochrophyta;Pelagophyceae;Pelagomonadales;uncultured_stramenopile
## 52                                 SILVA.v123_KJ759432.1.1798_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_III;uncultured_eukaryote
## 131                                SILVA.v123_EU793380.1.1676_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_syndiniales
## 45                                SILVA.v123_EU793930.1.1664_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_syndiniales
## 3                                       SILVA.v123_KJ763100.1.1794_Eukaryota;Haptophyta;Prymnesiophyceae;Prymnesiales;Braarudosphaera;uncultured_eukaryote
## 43                                   SILVA.v123_KJ763285.1.1791_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 5                                                               SILVA.v123_EF173010.1.1664_Eukaryota;SAR;Stramenopiles;MAST_1;MAST_1D;uncultured_eukaryote
## 62                                  SILVA.v123_KF129704.1.1753_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 98       SILVA.v123_AF525854.1.1776_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Micromonas;uncultured_marine_eukaryote
## 53                                   SILVA.v123_KJ763667.1.1784_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 125           SILVA.v123_KJ759460.1.1796_Eukaryota;SAR;Alveolata;Dinoflagellata;Dinophyceae;Gymnodiniphycidae;Kareniaceae;Karlodinium;uncultured_eukaryote
## 57                                                    SILVA.v123_KJ763141.1.1812_Eukaryota;SAR;Stramenopiles;Ochrophyta;Pelagophyceae;uncultured_eukaryote
## 108               SILVA.v123_AY955007.1.1727_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Micromonas;Micromonas_pusilla
## 21                                                      SILVA.v123_KF620989.1.1797_Eukaryota;Haptophyta;Prymnesiophyceae;Phaeocystis;uncultured_haptophyte
## 110             SILVA.v123_KF130557.1.1738_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Micromonas;uncultured_eukaryote
## 11                                               SILVA.v123_DQ310274.1.1563_Eukaryota;SAR;Stramenopiles;Bicosoecida;Pseudobodo;uncultured_marine_eukaryote
## 94                                            SILVA.v123_KC488456.1.1659_Eukaryota;Haptophyta;Prymnesiophyceae;Prymnesiales;OLI16029;uncultured_haptophyte
## 18                                 SILVA.v123_KJ759387.1.1799_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_III;uncultured_eukaryote
## 75                                                                    SILVA.v123_KJ763702.1.1796_Eukaryota;SAR;Rhizaria;Retaria;RAD_A;uncultured_eukaryote
## 9                                                    SILVA.v123_KJ763402.1.1791_Eukaryota;SAR;Alveolata;Dinoflagellata;Dinophyceae;B7;uncultured_eukaryote
## 31                                   SILVA.v123_KJ760589.1.1792_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 127                                 SILVA.v123_KF130519.1.1757_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 130                                  SILVA.v123_KF129962.1.1754_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 38                                             SILVA.v123_KJ762854.1.1799_Eukaryota;SAR;Alveolata;Dinoflagellata;Dinophyceae;SCM15C35;uncultured_eukaryote
## 140                                SILVA.v123_KJ759337.1.1800_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_III;uncultured_eukaryote
## 117                         SILVA.v123_FR874326.1.1777_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;uncultured_marine_picoeukaryote
## 58                                   SILVA.v123_KF130465.1.1754_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 19                                                  SILVA.v123_KJ763566.1.1798_Eukaryota;SAR;Alveolata;Dinoflagellata;Dinophyceae;B36;uncultured_eukaryote
## 40                         SILVA.v123_KJ759410.1.1799_Eukaryota;SAR;Alveolata;Dinoflagellata;Dinophyceae;Gymnodiniphycidae;Gyrodinium;uncultured_eukaryote
## 64                                                           SILVA.v123_GU823185.1.1396_Eukaryota;SAR;Stramenopiles;MAST_4;MAST_4F;uncultured_stramenopile
## 71                          SILVA.v123_KC488464.1.1700_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_III;uncultured_marine_alveolate
## 87                             SILVA.v123_AJ402349.1.1758_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_III;eukaryote_clone_OLI11005
## 67                                  SILVA.v123_KF130546.1.1757_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 113            SILVA.v123_FJ537303.1.1776_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Micromonas;uncultured_Micromonas
## 42                                             SILVA.v123_KJ763882.1.1802_Eukaryota;SAR;Alveolata;Dinoflagellata;Dinophyceae;SL163A10;uncultured_eukaryote
## 32                                   SILVA.v123_KJ762856.1.1793_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 51                                                                        SILVA.v123_KJ763625.1.1800_Eukaryota;SAR;Alveolata;SCM37C52;uncultured_eukaryote
## 59                                   SILVA.v123_KJ759527.1.1799_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 107             SILVA.v123_JF794050.1.1619_Eukaryota;SAR;Stramenopiles;Ochrophyta;Pelagophyceae;Sarcinochrysidales;Ankylochrisis;Pelagophyceae_sp._RCC2040
## 133                                         SILVA.v123_AM779755.1.1802_Eukaryota;Haptophyta;Prymnesiophyceae;Prymnesiales;Prymnesium;Prymnesium_palpebrale
## 97       SILVA.v123_HM581768.1.1760_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Micromonas;uncultured_marine_eukaryote
## 56                                  SILVA.v123_KJ763500.1.1801_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 20                                                                          SILVA.v123_JX188383.1.1765_Eukaryota;Picozoa;Picomonadida;uncultured_eukaryote
## 74                                  SILVA.v123_KJ763348.1.1800_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 2                                                            SILVA.v123_JQ781943.1.1807_Eukaryota;SAR;Stramenopiles;MAST_4;MAST_4F;uncultured_stramenopile
## 47                                      SILVA.v123_DQ369019.1.1798_Eukaryota;Haptophyta;Prymnesiophyceae;Prymnesiales;OLI16029;uncultured_marine_eukaryote
## 128                                  SILVA.v123_KJ759134.1.1789_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 86                                  SILVA.v123_KJ759592.1.1801_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 54                                                                          SILVA.v123_KC488339.1.1675_Eukaryota;Picozoa;Picomonadida;uncultured_biliphyte
## 28                                                       SILVA.v123_KJ760407.1.1804_Eukaryota;Haptophyta;Prymnesiophyceae;Phaeocystis;uncultured_eukaryote
## 12                                                           SILVA.v123_KJ759482.1.1801_Eukaryota;SAR;Stramenopiles;Ochrophyta;MOCH_2;uncultured_eukaryote
## 122 SILVA.v123_FR874360.1.1745_Eukaryota;SAR;Alveolata;Ciliophora;Intramacronucleata;Spirotrichea;Choreotrichia;uncultured;uncultured_marine_picoeukaryote
## 123                           SILVA.v123_KC582936.1.1795_Eukaryota;SAR;Alveolata;Dinoflagellata;Dinophyceae;Gymnodiniphycidae;SCM27C9;uncultured_alveolate
## 35                            SILVA.v123_JF826343.1.1605_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_marine_alveolate
## 139           SILVA.v123_KJ763684.1.1796_Eukaryota;SAR;Alveolata;Dinoflagellata;Dinophyceae;Gymnodiniphycidae;Kareniaceae;Karlodinium;uncultured_eukaryote
## 124                                 SILVA.v123_KJ760788.1.1795_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 119                                              SILVA.v123_AF280076.1.1787_Eukaryota;SAR;Alveolata;Protalveolata;Colpodellida;Voromonas;Voromonas_pontica
## 27            SILVA.v123_KJ763184.1.1781_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Ostreococcus;uncultured_eukaryote
## 114                                                      SILVA.v123_GQ863817.1.1709_Eukaryota;Haptophyta;Prymnesiophyceae;Phaeocystis;uncultured_eukaryote
## 1                                                            SILVA.v123_KJ759516.1.1803_Eukaryota;SAR;Stramenopiles;Ochrophyta;MOCH_2;uncultured_eukaryote
## 6                                                      SILVA.v123_AF180940.1.1800_Eukaryota;Haptophyta;Prymnesiophyceae;Phaeocystis;Phaeocystis_sp._PLY559
## 44                                  SILVA.v123_KF129645.1.1757_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 73                                        SILVA.v123_AY129063.1.1782_Eukaryota;SAR;Stramenopiles;Ochrophyta;Chrysophyceae;E222;uncultured_marine_eukaryote
## 49                                  SILVA.v123_JF790988.1.1777_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;Karlodinium_veneficum
## 33       SILVA.v123_GU820601.1.1201_Eukaryota;SAR;Alveolata;Dinoflagellata;Dinophyceae;Gymnodiniphycidae;Kareniaceae;Karlodinium;uncultured_dinoflagellate
## 142                           SILVA.v123_JF826317.1.1608_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_marine_alveolate
## 39                            SILVA.v123_KC488461.1.1687_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_marine_alveolate
## 82              SILVA.v123_GQ863805.1.1662_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Micromonas;uncultured_eukaryote
## 61                                                      SILVA.v123_KJ762999.1.1800_Eukaryota;Haptophyta;Prymnesiophyceae;Prymnesiales;uncultured_eukaryote
## 14                                  SILVA.v123_KJ759353.1.1798_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 111                                                     SILVA.v123_KF129692.1.1759_Eukaryota;Haptophyta;Prymnesiophyceae;Prymnesiales;uncultured_eukaryote
## 91                                                                  SILVA.v123_JQ781985.1.1807_Eukaryota;SAR;Stramenopiles;MAST_11;uncultured_stramenopile
## 15                                   SILVA.v123_KJ762893.1.1791_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 120                                 SILVA.v123_KJ759333.1.1794_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 69                                                           SILVA.v123_KC582982.1.1806_Eukaryota;SAR;Stramenopiles;MAST_4;MAST_4F;uncultured_stramenopile
## 77                                             SILVA.v123_KF129663.1.1757_Eukaryota;Haptophyta;Prymnesiophyceae;Prymnesiales;OLI16029;uncultured_eukaryote
## 37                       SILVA.v123_AF107080.1.1795_Eukaryota;Haptophyta;Prymnesiophyceae;Prymnesiales;OLI16029;unidentified_prymnesiophyte_clone_OLI16029
## 7                                    SILVA.v123_KF031588.1.1755_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 135                                  SILVA.v123_JX188306.1.1756_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_V;uncultured_eukaryote
## 129                                                          SILVA.v123_JQ782001.1.1776_Eukaryota;SAR;Stramenopiles;MAST_1;MAST_1B;uncultured_stramenopile
## 66                                  SILVA.v123_KC582940.1.1794_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_alveolate
## 17                                                  SILVA.v123_KJ763683.1.1799_Eukaryota;SAR;Alveolata;Dinoflagellata;Dinophyceae;B36;uncultured_eukaryote
## 25                                             SILVA.v123_KF130516.1.1755_Eukaryota;Haptophyta;Prymnesiophyceae;Prymnesiales;OLI51059;uncultured_eukaryote
## 34                                   SILVA.v123_KJ759300.1.1793_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_V;uncultured_eukaryote
## 100                                 SILVA.v123_KJ760584.1.1798_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 60                                   SILVA.v123_KF130084.1.1751_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 92                                   SILVA.v123_KJ760745.1.1794_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 22                                  SILVA.v123_KF130023.1.1761_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 90                                                                        SILVA.v123_KJ760345.1.1797_Eukaryota;SAR;Alveolata;SCM37C52;uncultured_eukaryote
## 63                                                                   SILVA.v123_JQ781946.1.1806_Eukaryota;SAR;Stramenopiles;MAST_4;uncultured_stramenopile
## 106           SILVA.v123_KJ762855.1.1768_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Ostreococcus;uncultured_eukaryote
## 118            SILVA.v123_KJ762455.1.1745_Eukaryota;SAR;Alveolata;Ciliophora;Intramacronucleata;Spirotrichea;Choreotrichia;uncultured;uncultured_eukaryote
## 136                                  SILVA.v123_KF129758.1.1746_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 36                    SILVA.v123_KC488605.1.1648_Eukaryota;SAR;Stramenopiles;Ochrophyta;Dictyochophyceae;Dictyochales;Florenciella;uncultured_stramenopile
## 8                                   SILVA.v123_KJ760603.1.1795_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 68                                                                   SILVA.v123_JQ782044.1.1803_Eukaryota;SAR;Stramenopiles;MAST_4;uncultured_stramenopile
## 46                                                                       SILVA.v123_GQ365865.1.1537_Eukaryota;Incertae_Sedis;Telonema;uncultured_eukaryote
## 48                                  SILVA.v123_KJ759424.1.1796_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 121                                  SILVA.v123_KF031747.1.1743_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 29                                   SILVA.v123_KJ759570.1.1784_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 24                                                      SILVA.v123_KF620977.1.1797_Eukaryota;Haptophyta;Prymnesiophyceae;Phaeocystis;uncultured_haptophyte

Number and roportion of regionally abundant OTUs (%):

## [1] 142
## [1] 2.498241


Cosmopolitan OTUs (relative abundance over 0.1% and occurence in more than 80% of samples):

##    otu_names mean_rabund perc_occur          classif
## 16   OTU_933 0.004796260   95.34884 Prymnesiophyceae
## 12    OTU_38 0.017451937   90.69767    Pelagophyceae
## 7   OTU_2200 0.003768490   90.69767             <NA>
## 11  OTU_3374 0.008484140   86.04651    Pelagophyceae
## 5   OTU_1921 0.003546814   86.04651 Prymnesiophyceae
## 3   OTU_1597 0.003304986   83.72093 Prymnesiophyceae
## 2   OTU_1456 0.002942243   83.72093      Dinophyceae
## 4   OTU_1833 0.002781025   83.72093             <NA>
## 13   OTU_380 0.001672645   83.72093 Prymnesiophyceae
## 10  OTU_3038 0.003103462   81.39535             <NA>
## 1   OTU_1383 0.003083310   81.39535             <NA>
## 14  OTU_4125 0.002519044   81.39535    Pelagophyceae
## 9   OTU_2553 0.001954778   81.39535             <NA>
## 8   OTU_2269 0.001813712   81.39535             <NA>
## 15   OTU_884 0.001531579   81.39535             <NA>
## 6   OTU_1997 0.001269598   81.39535 Prymnesiophyceae
##                                                                                                                                           OTUId
## 16                                            SILVA.v123_KJ763007.1.1798_Eukaryota;Haptophyta;Prymnesiophyceae;Phaeocystis;uncultured_eukaryote
## 12                         SILVA.v123_KF130487.1.1773_Eukaryota;SAR;Stramenopiles;Ochrophyta;Pelagophyceae;Pelagomonadales;uncultured_eukaryote
## 7                       SILVA.v123_KF130192.1.1763_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_III;uncultured_eukaryote
## 11 SILVA.v123_AC236360.17941.19743_Eukaryota;SAR;Stramenopiles;Ochrophyta;Pelagophyceae;Pelagomonadales;Aureococcus;Aureococcus_anophagefferens
## 5                                         SILVA.v123_HM581633.1.1797_Eukaryota;Haptophyta;Prymnesiophyceae;OLI16010;uncultured_marine_eukaryote
## 3                                                SILVA.v123_KJ762902.1.1800_Eukaryota;Haptophyta;Prymnesiophyceae;OLI16010;uncultured_eukaryote
## 2                                   SILVA.v123_KJ763154.1.1799_Eukaryota;SAR;Alveolata;Dinoflagellata;Dinophyceae;SCM15C35;uncultured_eukaryote
## 4                                                 SILVA.v123_JQ781940.1.1785_Eukaryota;SAR;Stramenopiles;MAST_1;MAST_1D;uncultured_stramenopile
## 13                                 SILVA.v123_KC488456.1.1659_Eukaryota;Haptophyta;Prymnesiophyceae;Prymnesiales;OLI16029;uncultured_haptophyte
## 10                        SILVA.v123_KJ763586.1.1789_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 1                                                              SILVA.v123_KJ763777.1.1804_Eukaryota;SAR;Alveolata;NIF_4C10;uncultured_eukaryote
## 14   SILVA.v123_JN934690.1.1635_Eukaryota;SAR;Stramenopiles;Ochrophyta;Pelagophyceae;Sarcinochrysidales;Ankylochrisis;Pelagophyceae_sp._RCC2505
## 9                       SILVA.v123_KJ759432.1.1798_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_III;uncultured_eukaryote
## 8                         SILVA.v123_KJ763285.1.1791_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 15                        SILVA.v123_KF129962.1.1754_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 6                                             SILVA.v123_KJ760407.1.1804_Eukaryota;Haptophyta;Prymnesiophyceae;Phaeocystis;uncultured_eukaryote

Number and proportion (%) of cosmopolitan OTUs:

## [1] 16
## [1] 0.2814919

Number and proportion (%) of rare OTUs:

## [1] 0
## [1] 0

1.6) Taxonomic composition analysis

1.6.1) Normalized data


PHOTOTROPHS + HETEROTROPHS

No. of OTUs and reads of the rearefied dataset:

## [1] 5684
## [1] 49622

No. of OTUs and reads of phototrophic groups:

## [1] 1895
## [1] 20050

No. of OTUs and reads of non-phototrophic groups:

## [1] 3789
## [1] 29572


Absolute values

##                          reads_per_class OTUs_per_class samples_per_class
## Bacillariophyceae                    297            135                39
## Bolidophyceae                        136             21                36
## Chlorarachniophyceae                 109             14                28
## Chlorophyceae                         22             16                14
## Chrysophyceae                        610            133                42
## Cryptophyceae                        381             56                26
## Dictyochophyceae                     644             47                43
## Dinophyceae                         5441           1026                43
## Eustigmatophyceae                     96             21                36
## Heterotrophs                       29572           3789                43
## Mamiellophyceae                     3166             99                37
## Nephroselmidophyceae                  18              6                13
## Pavlovophyceae                        48              6                25
## Pelagophyceae                       2195             21                43
## Phaeophyceae                           1              1                 1
## Prasinophyceae_clade-IX               63             13                17
## Prasinophyceae_clade-VII            1370             31                38
## Prymnesiophyceae                    5192            168                43
## Pyramimonadaceae                     100             16                23
## Rhodophyceae                           8              7                 7
## Trebouxiophyceae                      42             30                17
## Ulvophyceae                            2              2                 2
## Xanthophyceae                          4              4                 4
## other_Prasinophyceae                 105             22                32


Relative values

##   reads_per_class    OTUs_per_class samples_per_class 
##           100.000           100.000          1516.279
##                          reads_per_class OTUs_per_class samples_per_class
## Bacillariophyceae            0.598524848     2.37508797         90.697674
## Bolidophyceae                0.274071984     0.36945813         83.720930
## Chlorarachniophyceae         0.219660634     0.24630542         65.116279
## Chlorophyceae                0.044335174     0.28149191         32.558140
## Chrysophyceae                1.229293459     2.33990148         97.674419
## Cryptophyceae                0.767804603     0.98522167         60.465116
## Dictyochophyceae             1.297811455     0.82688248        100.000000
## Dinophyceae                 10.964894603    18.05066854        100.000000
## Eustigmatophyceae            0.193462577     0.36945813         83.720930
## Heterotrophs                59.594534682    66.66080225        100.000000
## Mamiellophyceae              6.380234573     1.74173118         86.046512
## Nephroselmidophyceae         0.036274233     0.10555947         30.232558
## Pavlovophyceae               0.096731289     0.10555947         58.139535
## Pelagophyceae                4.423441216     0.36945813        100.000000
## Phaeophyceae                 0.002015235     0.01759324          2.325581
## Prasinophyceae_clade-IX      0.126959816     0.22871217         39.534884
## Prasinophyceae_clade-VII     2.760872194     0.54539057         88.372093
## Prymnesiophyceae            10.463101044     2.95566502        100.000000
## Pyramimonadaceae             0.201523518     0.28149191         53.488372
## Rhodophyceae                 0.016121881     0.12315271         16.279070
## Trebouxiophyceae             0.084639877     0.52779733         39.534884
## Ulvophyceae                  0.004030470     0.03518649          4.651163
## Xanthophyceae                0.008060941     0.07037298          9.302326
## other_Prasinophyceae         0.211599694     0.38705137         74.418605



Reads per class vs. OTUs per class:



Reads per class vs. samples in which they occurr:


PHOTOTROPHS


Absolute values

##                          reads_per_class OTUs_per_class samples_per_class
## Bacillariophyceae                    297            135                39
## Bolidophyceae                        136             21                36
## Chlorarachniophyceae                 109             14                28
## Chlorophyceae                         22             16                14
## Chrysophyceae                        610            133                42
## Cryptophyceae                        381             56                26
## Dictyochophyceae                     644             47                43
## Dinophyceae                         5441           1026                43
## Eustigmatophyceae                     96             21                36
## Mamiellophyceae                     3166             99                37
## Nephroselmidophyceae                  18              6                13
## Pavlovophyceae                        48              6                25
## Pelagophyceae                       2195             21                43
## Phaeophyceae                           1              1                 1
## Prasinophyceae_clade-IX               63             13                17
## Prasinophyceae_clade-VII            1370             31                38
## Prymnesiophyceae                    5192            168                43
## Pyramimonadaceae                     100             16                23
## Rhodophyceae                           8              7                 7
## Trebouxiophyceae                      42             30                17
## Ulvophyceae                            2              2                 2
## Xanthophyceae                          4              4                 4
## other_Prasinophyceae                 105             22                32


Relative values

##   reads_per_class    OTUs_per_class samples_per_class 
##           100.000           100.000          1416.279
##                          reads_per_class OTUs_per_class samples_per_class
## Bacillariophyceae            1.481296758     7.12401055         90.697674
## Bolidophyceae                0.678304239     1.10817942         83.720930
## Chlorarachniophyceae         0.543640898     0.73878628         65.116279
## Chlorophyceae                0.109725686     0.84432718         32.558140
## Chrysophyceae                3.042394015     7.01846966         97.674419
## Cryptophyceae                1.900249377     2.95514512         60.465116
## Dictyochophyceae             3.211970075     2.48021108        100.000000
## Dinophyceae                 27.137157107    54.14248021        100.000000
## Eustigmatophyceae            0.478802993     1.10817942         83.720930
## Mamiellophyceae             15.790523691     5.22427441         86.046512
## Nephroselmidophyceae         0.089775561     0.31662269         30.232558
## Pavlovophyceae               0.239401496     0.31662269         58.139535
## Pelagophyceae               10.947630923     1.10817942        100.000000
## Phaeophyceae                 0.004987531     0.05277045          2.325581
## Prasinophyceae_clade-IX      0.314214464     0.68601583         39.534884
## Prasinophyceae_clade-VII     6.832917706     1.63588391         88.372093
## Prymnesiophyceae            25.895261845     8.86543536        100.000000
## Pyramimonadaceae             0.498753117     0.84432718         53.488372
## Rhodophyceae                 0.039900249     0.36939314         16.279070
## Trebouxiophyceae             0.209476309     1.58311346         39.534884
## Ulvophyceae                  0.009975062     0.10554090          4.651163
## Xanthophyceae                0.019950125     0.21108179          9.302326
## other_Prasinophyceae         0.523690773     1.16094987         74.418605



Reads per class vs. OTUs per class:



Reads per class vs. samples in which they occurr:

1.6.2) Non-rarefied data


PHOTOTROPHS + HETEROTROPHS

No. of OTUs and reads of the rearefied dataset:

## [1] 8349
## [1] 223622

No. of OTUs and reads of phototrophic groups:

## [1] 2882
## [1] 100242

No. of OTUs and reads of non-phototrophic groups:

## [1] 5467
## [1] 123380


Absolute values

##                              reads_per_class OTUs_per_class
## Bacillariophyceae                       2664            374
## Bolidophyceae                            509             25
## Chlorarachniophyceae                     327             20
## Chlorophyceae                             79             45
## Chrysophyceae                           2824            240
## Cryptophyceae                           1922             95
## Dictyochophyceae                        2819             52
## Dinophyceae                            23637           1476
## Eustigmatophyceae                        359             27
## Heterotrophs                          123380           5467
## IncertaeSedis_Archaeplastida               1              1
## Mamiellophyceae                        15846            117
## Nephroselmidophyceae                      64              7
## Pavlovophyceae                           228             13
## Pelagophyceae                           9306             25
## Phaeophyceae                               5              4
## Phaeothamniophyceae                        1              1
## Prasinophyceae_clade-IX                  155             16
## Prasinophyceae_clade-VII                3575             37
## Prymnesiophyceae                       34758            177
## Pyramimonadaceae                         507             19
## Rhodophyceae                              16             12
## Trebouxiophyceae                         121             57
## Ulvophyceae                                6              5
## Xanthophyceae                             21             11
## other_Prasinophyceae                     492             26
##                              samples_per_class
## Bacillariophyceae                           42
## Bolidophyceae                               43
## Chlorarachniophyceae                        41
## Chlorophyceae                               26
## Chrysophyceae                               43
## Cryptophyceae                               39
## Dictyochophyceae                            43
## Dinophyceae                                 43
## Eustigmatophyceae                           42
## Heterotrophs                                43
## IncertaeSedis_Archaeplastida                 1
## Mamiellophyceae                             41
## Nephroselmidophyceae                        19
## Pavlovophyceae                              37
## Pelagophyceae                               43
## Phaeophyceae                                 4
## Phaeothamniophyceae                          1
## Prasinophyceae_clade-IX                     29
## Prasinophyceae_clade-VII                    42
## Prymnesiophyceae                            43
## Pyramimonadaceae                            33
## Rhodophyceae                                13
## Trebouxiophyceae                            26
## Ulvophyceae                                  3
## Xanthophyceae                               14
## other_Prasinophyceae                        41


Relative values

##   reads_per_class    OTUs_per_class samples_per_class 
##           100.000           100.000          1848.837
##                              reads_per_class OTUs_per_class
## Bacillariophyceae               1.191296e+00     4.47957839
## Bolidophyceae                   2.276162e-01     0.29943706
## Chlorarachniophyceae            1.462289e-01     0.23954965
## Chlorophyceae                   3.532747e-02     0.53898670
## Chrysophyceae                   1.262845e+00     2.87459576
## Cryptophyceae                   8.594861e-01     1.13786082
## Dictyochophyceae                1.260609e+00     0.62282908
## Dinophyceae                     1.057007e+01    17.67876392
## Eustigmatophyceae               1.605388e-01     0.32339202
## Heterotrophs                    5.517346e+01    65.48089592
## IncertaeSedis_Archaeplastida    4.471832e-04     0.01197748
## Mamiellophyceae                 7.086065e+00     1.40136543
## Nephroselmidophyceae            2.861972e-02     0.08384238
## Pavlovophyceae                  1.019578e-01     0.15570727
## Pelagophyceae                   4.161487e+00     0.29943706
## Phaeophyceae                    2.235916e-03     0.04790993
## Phaeothamniophyceae             4.471832e-04     0.01197748
## Prasinophyceae_clade-IX         6.931339e-02     0.19163972
## Prasinophyceae_clade-VII        1.598680e+00     0.44316685
## Prymnesiophyceae                1.554319e+01     2.12001437
## Pyramimonadaceae                2.267219e-01     0.22757216
## Rhodophyceae                    7.154931e-03     0.14372979
## Trebouxiophyceae                5.410917e-02     0.68271649
## Ulvophyceae                     2.683099e-03     0.05988741
## Xanthophyceae                   9.390847e-03     0.13175231
## other_Prasinophyceae            2.200141e-01     0.31141454
##                              samples_per_class
## Bacillariophyceae                    97.674419
## Bolidophyceae                       100.000000
## Chlorarachniophyceae                 95.348837
## Chlorophyceae                        60.465116
## Chrysophyceae                       100.000000
## Cryptophyceae                        90.697674
## Dictyochophyceae                    100.000000
## Dinophyceae                         100.000000
## Eustigmatophyceae                    97.674419
## Heterotrophs                        100.000000
## IncertaeSedis_Archaeplastida          2.325581
## Mamiellophyceae                      95.348837
## Nephroselmidophyceae                 44.186047
## Pavlovophyceae                       86.046512
## Pelagophyceae                       100.000000
## Phaeophyceae                          9.302326
## Phaeothamniophyceae                   2.325581
## Prasinophyceae_clade-IX              67.441860
## Prasinophyceae_clade-VII             97.674419
## Prymnesiophyceae                    100.000000
## Pyramimonadaceae                     76.744186
## Rhodophyceae                         30.232558
## Trebouxiophyceae                     60.465116
## Ulvophyceae                           6.976744
## Xanthophyceae                        32.558140
## other_Prasinophyceae                 95.348837



Reads per class vs. OTUs per class:



Reads per class vs. samples in which they occurr:


PHOTOTROPHS


Absolute values

##                              reads_per_class OTUs_per_class
## Bacillariophyceae                       2664            374
## Bolidophyceae                            509             25
## Chlorarachniophyceae                     327             20
## Chlorophyceae                             79             45
## Chrysophyceae                           2824            240
## Cryptophyceae                           1922             95
## Dictyochophyceae                        2819             52
## Dinophyceae                            23637           1476
## Eustigmatophyceae                        359             27
## IncertaeSedis_Archaeplastida               1              1
## Mamiellophyceae                        15846            117
## Nephroselmidophyceae                      64              7
## Pavlovophyceae                           228             13
## Pelagophyceae                           9306             25
## Phaeophyceae                               5              4
## Phaeothamniophyceae                        1              1
## Prasinophyceae_clade-IX                  155             16
## Prasinophyceae_clade-VII                3575             37
## Prymnesiophyceae                       34758            177
## Pyramimonadaceae                         507             19
## Rhodophyceae                              16             12
## Trebouxiophyceae                         121             57
## Ulvophyceae                                6              5
## Xanthophyceae                             21             11
## other_Prasinophyceae                     492             26
##                              samples_per_class
## Bacillariophyceae                           42
## Bolidophyceae                               43
## Chlorarachniophyceae                        41
## Chlorophyceae                               26
## Chrysophyceae                               43
## Cryptophyceae                               39
## Dictyochophyceae                            43
## Dinophyceae                                 43
## Eustigmatophyceae                           42
## IncertaeSedis_Archaeplastida                 1
## Mamiellophyceae                             41
## Nephroselmidophyceae                        19
## Pavlovophyceae                              37
## Pelagophyceae                               43
## Phaeophyceae                                 4
## Phaeothamniophyceae                          1
## Prasinophyceae_clade-IX                     29
## Prasinophyceae_clade-VII                    42
## Prymnesiophyceae                            43
## Pyramimonadaceae                            33
## Rhodophyceae                                13
## Trebouxiophyceae                            26
## Ulvophyceae                                  3
## Xanthophyceae                               14
## other_Prasinophyceae                        41


Relative values

##   reads_per_class    OTUs_per_class samples_per_class 
##           100.000           100.000          1748.837
##                              reads_per_class OTUs_per_class
## Bacillariophyceae               2.657569e+00    12.97709924
## Bolidophyceae                   5.077712e-01     0.86745316
## Chlorarachniophyceae            3.262106e-01     0.69396253
## Chlorophyceae                   7.880928e-02     1.56141568
## Chrysophyceae                   2.817182e+00     8.32755031
## Cryptophyceae                   1.917360e+00     3.29632200
## Dictyochophyceae                2.812194e+00     1.80430257
## Dinophyceae                     2.357994e+01    51.21443442
## Eustigmatophyceae               3.581333e-01     0.93684941
## IncertaeSedis_Archaeplastida    9.975858e-04     0.03469813
## Mamiellophyceae                 1.580775e+01     4.05968078
## Nephroselmidophyceae            6.384549e-02     0.24288688
## Pavlovophyceae                  2.274496e-01     0.45107564
## Pelagophyceae                   9.283534e+00     0.86745316
## Phaeophyceae                    4.987929e-03     0.13879251
## Phaeothamniophyceae             9.975858e-04     0.03469813
## Prasinophyceae_clade-IX         1.546258e-01     0.55517002
## Prasinophyceae_clade-VII        3.566369e+00     1.28383067
## Prymnesiophyceae                3.467409e+01     6.14156836
## Pyramimonadaceae                5.057760e-01     0.65926440
## Rhodophyceae                    1.596137e-02     0.41637752
## Trebouxiophyceae                1.207079e-01     1.97779320
## Ulvophyceae                     5.985515e-03     0.17349063
## Xanthophyceae                   2.094930e-02     0.38167939
## other_Prasinophyceae            4.908122e-01     0.90215128
##                              samples_per_class
## Bacillariophyceae                    97.674419
## Bolidophyceae                       100.000000
## Chlorarachniophyceae                 95.348837
## Chlorophyceae                        60.465116
## Chrysophyceae                       100.000000
## Cryptophyceae                        90.697674
## Dictyochophyceae                    100.000000
## Dinophyceae                         100.000000
## Eustigmatophyceae                    97.674419
## IncertaeSedis_Archaeplastida          2.325581
## Mamiellophyceae                      95.348837
## Nephroselmidophyceae                 44.186047
## Pavlovophyceae                       86.046512
## Pelagophyceae                       100.000000
## Phaeophyceae                          9.302326
## Phaeothamniophyceae                   2.325581
## Prasinophyceae_clade-IX              67.441860
## Prasinophyceae_clade-VII             97.674419
## Prymnesiophyceae                    100.000000
## Pyramimonadaceae                     76.744186
## Rhodophyceae                         30.232558
## Trebouxiophyceae                     60.465116
## Ulvophyceae                           6.976744
## Xanthophyceae                        32.558140
## other_Prasinophyceae                 95.348837



Reads per class vs. OTUs per class:



Reads per class vs. samples in which they occurr:





2) 16S amplicons

2.1) Data overview

Let’s read the dataset and remove the samples containing less than 36155 reads:

Table dimensions and content outline:

## [1] 28294    43
##       TARA_102_SUR_0d2_3 TARA_109_SUR_0d2_3 TARA_110_SUR_0d2_3
## OTU_1                  0                  1                  0
## OTU_2                  0                  0                  0
## OTU_3                  0                  0                  0
## OTU_4                  2                  3                  1
## OTU_5                  0                  0                  0
##       TARA_111_SUR_0d2_3 TARA_112_SUR_0d2_3
## OTU_1                  0                  1
## OTU_2                  0                  0
## OTU_3                  0                  0
## OTU_4                  5                  2
## OTU_5                  0                  0

Minimum number of reads per station:

min(colSums(tb16_tax_occur_min36155)) 
## [1] 36155

Maximum number of reads per station:

max(colSums(tb16_tax_occur_min36155)) 
## [1] 158933

Identification of stations with higher number of reads:

amplicons_per_sample<-colSums(tb16_tax_occur_min36155)
amplicons_per_sample[which(colSums(tb16_tax_occur_min36155)>150000)]
## TARA_64_SUR_0d2_3 TARA_85_SUR_0d2_3 
##            158933            150654

Overall reads per sample:

2.2) Normalization

Let’s normalize the original dataset by randomly subsampling 36155 reads in each station:

tb16_tax_occur_min36155_t<-t(tb16_tax_occur_min36155)
tb16_tax_occur_ss36155<-rrarefy(tb16_tax_occur_min36155_t, 36155)

The normalized table shows the following dimensions and format:

## [1]    43 28294
##                    OTU_1 OTU_2 OTU_3 OTU_4 OTU_5
## TARA_102_SUR_0d2_3     0     0     0     1     0
## TARA_109_SUR_0d2_3     1     0     0     2     0
## TARA_110_SUR_0d2_3     0     0     0     1     0
## TARA_111_SUR_0d2_3     0     0     0     1     0
## TARA_112_SUR_0d2_3     0     0     0     0     0

Its content fits with the expected normalization values (36155 reads per station):

rowSums(tb16_tax_occur_ss36155)
## TARA_102_SUR_0d2_3 TARA_109_SUR_0d2_3 TARA_110_SUR_0d2_3 
##              36155              36155              36155 
## TARA_111_SUR_0d2_3 TARA_112_SUR_0d2_3 TARA_122_SUR_0d2_3 
##              36155              36155              36155 
## TARA_123_SUR_0d2_3 TARA_124_SUR_0d2_3 TARA_125_SUR_0d2_3 
##              36155              36155              36155 
## TARA_128_SUR_0d2_3 TARA_132_SUR_0d2_3 TARA_133_SUR_0d2_3 
##              36155              36155              36155 
## TARA_137_SUR_0d2_3 TARA_138_SUR_0d2_3 TARA_140_SUR_0d2_3 
##              36155              36155              36155 
## TARA_142_SUR_0d2_3 TARA_145_SUR_0d2_3 TARA_146_SUR_0d2_3 
##              36155              36155              36155 
## TARA_148_SUR_0d2_3 TARA_149_SUR_0d2_3 TARA_150_SUR_0d2_3 
##              36155              36155              36155 
## TARA_151_SUR_0d2_3 TARA_152_SUR_0d2_3  TARA_56_SUR_0d2_3 
##              36155              36155              36155 
##  TARA_57_SUR_0d2_3  TARA_62_SUR_0d2_3  TARA_64_SUR_0d2_3 
##              36155              36155              36155 
##  TARA_65_SUR_0d2_3  TARA_66_SUR_0d2_3  TARA_68_SUR_0d2_3 
##              36155              36155              36155 
##  TARA_72_SUR_0d2_3  TARA_76_SUR_0d2_3  TARA_78_SUR_0d2_3 
##              36155              36155              36155 
##  TARA_82_SUR_0d2_3  TARA_84_SUR_0d2_3  TARA_85_SUR_0d2_3 
##              36155              36155              36155 
##  TARA_96_SUR_0d2_3  TARA_98_SUR_0d2_3  TARA_99_SUR_0d2_3 
##              36155              36155              36155 
##             MP0311             MP1517             MP1672 
##              36155              36155              36155 
##             MP2821 
##              36155

Let’s check out how many OTUs don’t appear in the new table:

length(which(colSums(tb16_tax_occur_ss36155)==0))
## [1] 8568

There are 8045 OTUs that don’t show any occurrence in the normalized data. Let’s remove them from the table and take a look at its final dimensions:

tb16_tax_occur_ss36155_no_cero<-tb16_tax_occur_ss36155[,-(which(colSums(tb16_tax_occur_ss36155)==0))]
tb16_tax_occur_ss36155_no_cero<-tb16_tax_occur_ss36155_no_cero[mixedorder(row.names(tb16_tax_occur_ss36155_no_cero)),]
dim(tb16_tax_occur_ss36155_no_cero)
## [1]    43 19726

Datasets summary:

dim(tb16_tax)
## [1] 28294    58
dim(tb16_tax_occur)
## [1] 28294    55
dim(tb16_tax_occur_ss36155_no_cero)
## [1]    43 19726
#28294    58
#28294    55
#43 19726

2.3) General community analysis

2.3.1) Richness and evenness (Shannon index)

Most of the samples take Shannon Index values around 6:

2.3.2) Richness: OTU number

Lowest number of OTUs per sample:

## [1] 2503

Maximum number of OTUs per sample:

## [1] 5092

In most of the samples, we can identify between 600 and 700 OTUs:

plot(sort(OTUs_per_sample_16S_tax_occur_ss36155), pch=19)

boxplot(OTUs_per_sample_16S_tax_occur_ss36155, pch=19)

2.3.3) Index of evenness

2.3.3.1) Pielou’s index

pielou_evenness_16S_tax_occur_ss36155<-tb16_tax_occur_ss36155_div/log(OTUs_per_sample_16S_tax_occur_ss36155)

The Pielou index (constrained between 0 and 1) takes values closer to 1 as the variation of species proportion in a sample increases. Most of the samples get values around 0.95, meaning that the numerical composition of different OTUs in a sample is highly variable - there’s no constant presence of dominant species.

The less variation in communities between the species (and the presence of a dominant specie), the lower J’ is.

plot(sort(pielou_evenness_16S_tax_occur_ss36155), pch=19)

boxplot(pielou_evenness_16S_tax_occur_ss36155, pch=19)

The OTU_38, with 874 reads, is the most abundant in the overall dataset:

head(sort(colSums(tb16_tax_occur_ss36155_no_cero), decreasing=T), n=10L)
## OTU_1754 OTU_2893  OTU_761 OTU_2428 OTU_3736 OTU_1942 OTU_2466 OTU_3271 
##    17121    13628    13145    12010    11106    10244    10043     8626 
## OTU_5398 OTU_5330 
##     8526     7736

Most of the OTUs show very few occurrences; suggesting that we will probably be able to identify a significant ammount of rare otus:

plot(log(sort(colSums(tb16_tax_occur_ss36155_no_cero), decreasing=T)), pch=19)

2.3.4) Abundance Models

2.3.4.1) Rank-Abundance or Dominance/Diversity Model (“radfit”)

The OTUs abundance distribution fits relativelly close to log-normal model.

2.3.4.2) Preston’s Lognormal Model

According to Preston’s lognormal model fit into species frequencies groups, we’re missing 1588.816 species:

tb16_tax_occur_ss36155_prestonfit<-prestonfit(colSums(tb16_tax_occur_min36155_t))
plot(tb16_tax_occur_ss36155_prestonfit, main="Pooled species")

veiledspec(tb16_tax_occur_ss36155_prestonfit)
## Extrapolated     Observed       Veiled 
##     108452.1      24691.0      83761.1

When computing Prestons’ lognormal model fit without pooling data into groups, we seem to miss 1385.371 species:

## Extrapolated     Observed       Veiled 
##     75267.64     24691.00     50576.64

2.3.5) Rarefaction curves of rarefied and non-rarefied datasets

rarec_input<-t(as.matrix(colSums(tb16_tax_occur_ss36155_no_cero)))

#tb16_rarecurve_step1000_10000<-rarecurve(rarec_input, step = 1000, 10000, xlab = "Sample size", ylab = "OTUs", label = TRUE, main="16S amplicons diversity step=1000 & ss=10000\n(40,816 OTUs; 5,247,375 reads)\n")
#tb16_rarecurve_step1000_10000

tb16_rarecurve_step100_5700<-rarecurve(rarec_input, step = 1000, 19700, xlab = "Sample size", ylab = "OTUs", label = TRUE, main="16S amplicons diversity step=100 & ss=5700\n(19,756 OTUs; 1,554,665 reads)\n")

#without rarefying
rarec_allOTUs_input<-t(as.matrix(colSums(t(tb16_tax_occur))))
tb16_rarecurve_allOTUs_step100_8642<-rarecurve(rarec_allOTUs_input, step = 1000, 28200, xlab = "Sample size", ylab = "OTUs", label = TRUE, main="16S amplicons diversity non-rarefied step=1000 & ss=100000\n(28,294 OTUs; 4,285,523 reads)\n")

2.3.6) Beta diversity

2.3.6.1) Dissimilarity matrix using Bray-Curtis index:

The Bray-Curtis dissimilarity, constrained between 0 (minimum distance) and 1 (highest dissimilarity) allows us to quantify the differences between samples according to the composition and relative abundance of their OTUs. In our dataset, most of the samples pairs take dissimilarity values around 0.8, meaning that their composition is substantially different.

2.3.6.2) Hierarchical clustering

The stations seem to form clusters according to geographic localization, but there are no evident clusters separated from the general groups, apart from the one containing TARA_84, TARA_82 and TARA_85.

(To be done: assign Longhurst provinces information to each station and check if any of the central clusters is meaningful regarding to the samples’ geographical location)

2.3.6.3) Non-metric multidimensional scaling

We can identify a prominent group in the central part of the NMDS plot and a few outliers (TARA 82, 84 and 85) in the central-right edge of the plot. The stress parameter takes a value below 0.2, suggesting that the plot is acceptable.

## 
## Call:
## monoMDS(dist = tb16_tax_occur_ss36155_no_cero.bray) 
## 
## Non-metric Multidimensional Scaling
## 
## 43 points, dissimilarity 'bray', call 'vegdist(x = tb16_tax_occur_ss36155_no_cero, method = "bray")'
## 
## Dimensions: 2 
## Stress:     9.589501e-05 
## Stress type 1, weak ties
## Scores scaled to unit root mean square, rotated to principal components
## Stopped after 62 iterations: Stress nearly zero (< smin)

When implementing a most robut function for computing NMDS plots, the result is quiet the same:

## Run 0 stress 9.301068e-05 
## Run 1 stress 9.158128e-05 
## ... New best solution
## ... Procrustes: rmse 5.375076e-05  max resid 0.0002756587 
## ... Similar to previous best
## Run 2 stress 9.428448e-05 
## ... Procrustes: rmse 2.781509e-05  max resid 0.0001387135 
## ... Similar to previous best
## Run 3 stress 9.332153e-05 
## ... Procrustes: rmse 0.0001081792  max resid 0.0003003597 
## ... Similar to previous best
## Run 4 stress 9.620788e-05 
## ... Procrustes: rmse 7.880078e-05  max resid 0.0002958135 
## ... Similar to previous best
## Run 5 stress 7.292808e-05 
## ... New best solution
## ... Procrustes: rmse 8.029629e-05  max resid 0.0002395264 
## ... Similar to previous best
## Run 6 stress 9.457543e-05 
## ... Procrustes: rmse 9.02236e-05  max resid 0.0002043675 
## ... Similar to previous best
## Run 7 stress 9.195291e-05 
## ... Procrustes: rmse 7.181292e-05  max resid 0.0001653436 
## ... Similar to previous best
## Run 8 stress 9.669817e-05 
## ... Procrustes: rmse 8.197419e-05  max resid 0.0002534159 
## ... Similar to previous best
## Run 9 stress 9.961385e-05 
## ... Procrustes: rmse 5.636359e-05  max resid 0.0001619826 
## ... Similar to previous best
## Run 10 stress 9.64433e-05 
## ... Procrustes: rmse 8.938231e-05  max resid 0.0002629114 
## ... Similar to previous best
## Run 11 stress 7.614704e-05 
## ... Procrustes: rmse 7.66202e-05  max resid 0.0002242664 
## ... Similar to previous best
## Run 12 stress 9.185541e-05 
## ... Procrustes: rmse 5.891344e-05  max resid 0.0002376396 
## ... Similar to previous best
## Run 13 stress 7.979814e-05 
## ... Procrustes: rmse 7.351333e-05  max resid 0.0001877524 
## ... Similar to previous best
## Run 14 stress 9.896201e-05 
## ... Procrustes: rmse 9.046256e-05  max resid 0.0002714003 
## ... Similar to previous best
## Run 15 stress 9.814128e-05 
## ... Procrustes: rmse 2.413431e-05  max resid 7.570832e-05 
## ... Similar to previous best
## Run 16 stress 9.22882e-05 
## ... Procrustes: rmse 8.985092e-05  max resid 0.0002411534 
## ... Similar to previous best
## Run 17 stress 9.977628e-05 
## ... Procrustes: rmse 9.592451e-05  max resid 0.000260223 
## ... Similar to previous best
## Run 18 stress 9.807055e-05 
## ... Procrustes: rmse 8.39958e-05  max resid 0.00019424 
## ... Similar to previous best
## Run 19 stress 9.558017e-05 
## ... Procrustes: rmse 3.817104e-05  max resid 0.0001220175 
## ... Similar to previous best
## Run 20 stress 9.839229e-05 
## ... Procrustes: rmse 4.602517e-05  max resid 0.0001242549 
## ... Similar to previous best
## *** Solution reached
## Warning in metaMDS(tb16_tax_occur_ss36155_no_cero.bray): Stress is (nearly)
## zero - you may have insufficient data
## Warning in ordiplot(x, choices = choices, type = type, display = display, :
## Species scores not available

2.4) Geographical analysis

## Warning in if (class(lats) == "SpatialPoints") lats <- coordinates(lats):
## the condition has length > 1 and only the first element will be used

Working datasets:

  1. Community matrix: tb16_tax_occur_ss36155_no_cero
dim(tb16_tax_occur_ss36155_no_cero)
## [1]    43 19763
tb16_tax_occur_ss36155_no_cero[1:5, 1:5]
##                    OTU_1 OTU_3 OTU_4 OTU_5 OTU_7
## MP0311                 0     0     0     0     0
## MP1517                 0     0     3     0     1
## MP1672                 0     0     0     0     0
## MP2821                 1     0     0     0     1
## TARA_102_SUR_0d2_3     0     0     1     0     0
  1. Community Bray-Curtis: tb16_tax_occur_ss36155_no_cero.bray
tb16_tax_occur_ss36155_no_cero.bray<-as.matrix(tb16_tax_occur_ss36155_no_cero.bray)
## [1] 43 43
  1. Stations distances in km: geo_distances_MP_16S
dim(geo_distances_MP_16S)
## [1] 43 43

Communities quickly change their composition across geographical distances:

plot(geo_distances_MP_16S, tb16_tax_occur_ss36155_no_cero.bray, pch=19, cex=0.4, xlab="Geopgraphical distances", ylab="Bray-Curtis dissimilarities")

2.4.1) Mantel correlograms

Mantel statistic is -significantlly- so low, meaning that the correlation between samples dissimilarity and geographical distances is weak.

mantel(geo_distances_MP_16S, tb16_tax_occur_ss36155_no_cero.bray)
## 
## Mantel statistic based on Pearson's product-moment correlation 
## 
## Call:
## mantel(xdis = geo_distances_MP_16S, ydis = tb16_tax_occur_ss36155_no_cero.bray) 
## 
## Mantel statistic r: 0.02826 
##       Significance: 0.279 
## 
## Upper quantiles of permutations (null model):
##    90%    95%  97.5%    99% 
## 0.0873 0.1167 0.1444 0.1697 
## Permutation: free
## Number of permutations: 999

Maximum distance between samples:

## [1] 19543.94

Minimum distance between samples:

## [1] 0

Correlograms:

MP_16s_ss36155_mantel_correl_by_1000km<-mantel.correlog(tb16_tax_occur_ss36155_no_cero.bray, D.geo=geo_distances_MP_16S, break.pts=seq(0,20000, by=1000))
plot(MP_16s_ss36155_mantel_correl_by_1000km)

MP_16s_ss36155_mantel_correl_by_100km<-mantel.correlog(tb16_tax_occur_ss36155_no_cero.bray, D.geo=geo_distances_MP_16S, break.pts=seq(0,20000, by=100))
plot(MP_16s_ss36155_mantel_correl_by_100km)

2.5) Abundance vs. occurence

In the following plot, we can appreciate the OTUs distribution according to their percentage of occurence and relative abundance. The red line keeps up OTUs that occur in more than 80% of the samples, the green line limits regionally rare OTUs (< 0.001%), and the blue one restricts regionally abundant OTUs (> 0.1%).

Regionally abundant OTUs (relative abundance over 0.1%):

tb16_class_prov<-cbind(otu_names=row.names(tb16_class),tb16_class)
##     otu_names mean_rabund perc_occur          class_B
## 1   OTU_10747 0.001144941   55.81395   other_bacteria
## 2   OTU_12129 0.001116639   65.11628    Synechococcus
## 3    OTU_1329 0.002241640   93.02326   other_bacteria
## 4    OTU_1676 0.002044814   88.37209  Prochlorococcus
## 5    OTU_1738 0.001929676   93.02326   other_bacteria
## 6    OTU_1754 0.011149026   93.02326  Prochlorococcus
## 7    OTU_1942 0.006453480   93.02326  Prochlorococcus
## 8     OTU_223 0.001027231   93.02326   other_bacteria
## 9      OTU_23 0.001443398   93.02326   other_bacteria
## 10   OTU_2428 0.007645377   93.02326   other_bacteria
## 11   OTU_2466 0.006429681   93.02326  Prochlorococcus
## 12   OTU_2789 0.001014366  100.00000   other_bacteria
## 13  OTU_27900 0.002379934  100.00000 Prymnesiophyceae
## 14  OTU_27901 0.003573117   81.39535 Prymnesiophyceae
## 15  OTU_27912 0.001820971   46.51163 Prymnesiophyceae
## 16  OTU_27927 0.003777663   48.83721  Mamiellophyceae
## 17  OTU_27934 0.001615139   95.34884 Prymnesiophyceae
## 18  OTU_27938 0.001353989   93.02326    Pelagophyceae
## 19  OTU_28017 0.001251717   79.06977    Pelagophyceae
## 20  OTU_28046 0.001222771   55.81395  Mamiellophyceae
## 21  OTU_28060 0.001001502   41.86047  Mamiellophyceae
## 22  OTU_28061 0.002150302   51.16279  Mamiellophyceae
## 23   OTU_2866 0.003430321   90.69767   other_bacteria
## 24   OTU_2877 0.002066683   95.34884   other_bacteria
## 25   OTU_2893 0.008587059   93.02326   other_bacteria
## 26     OTU_29 0.002464840  100.00000   other_bacteria
## 27   OTU_2980 0.001006648  100.00000   other_bacteria
## 28   OTU_3004 0.002071829   93.02326   other_bacteria
## 29   OTU_3023 0.001958621   93.02326   other_bacteria
## 30   OTU_3162 0.002286023   95.34884   other_bacteria
## 31   OTU_3172 0.002888082   88.37209   other_bacteria
## 32   OTU_3173 0.001013080   83.72093   other_bacteria
## 33   OTU_3187 0.003630364  100.00000   other_bacteria
## 34   OTU_3197 0.001815825   81.39535   other_bacteria
## 35   OTU_3198 0.001436966   93.02326   other_bacteria
## 36   OTU_3207 0.001030447   90.69767   other_bacteria
## 37   OTU_3214 0.001204761   93.02326   other_bacteria
## 38   OTU_3240 0.001783021   93.02326   other_bacteria
## 39   OTU_3259 0.002529805   58.13953   other_bacteria
## 40   OTU_3271 0.005586413   90.69767  Prochlorococcus
## 41   OTU_3308 0.002082121   97.67442    Synechococcus
## 42   OTU_3311 0.002843056   90.69767  Prochlorococcus
## 43   OTU_3326 0.001315396   90.69767   other_bacteria
## 44    OTU_333 0.001588123  100.00000   other_bacteria
## 45   OTU_3347 0.001297386   97.67442   other_bacteria
## 46   OTU_3680 0.001653732   93.02326   other_bacteria
## 47   OTU_3731 0.001496142  100.00000   other_bacteria
## 48   OTU_3736 0.007181611   93.02326  Prochlorococcus
## 49   OTU_3789 0.001064538  100.00000   other_bacteria
## 50   OTU_3803 0.001385507  100.00000   other_bacteria
## 51   OTU_3810 0.001757292   93.02326   other_bacteria
## 52   OTU_4036 0.001322471   97.67442   other_bacteria
## 53   OTU_4048 0.002347129  100.00000   other_bacteria
## 54   OTU_4083 0.001072257   95.34884   other_bacteria
## 55   OTU_4366 0.001663381  100.00000   other_bacteria
## 56   OTU_4560 0.001658878  100.00000   other_bacteria
## 57   OTU_4664 0.001741211  100.00000   other_bacteria
## 58   OTU_4926 0.001751503   93.02326   other_bacteria
## 59   OTU_4991 0.001551460   95.34884   other_bacteria
## 60    OTU_520 0.001058749   93.02326   other_bacteria
## 61   OTU_5211 0.001081262   95.34884   other_bacteria
## 62   OTU_5222 0.001090910   93.02326   other_bacteria
## 63   OTU_5266 0.001177102   93.02326   other_bacteria
## 64   OTU_5268 0.001193826  100.00000   other_bacteria
## 65   OTU_5288 0.001213123   90.69767  Prochlorococcus
## 66   OTU_5301 0.001794599   95.34884   other_bacteria
## 67   OTU_5327 0.001590696   93.02326   other_bacteria
## 68   OTU_5330 0.004964414   93.02326  Prochlorococcus
## 69   OTU_5352 0.003766728   58.13953   other_bacteria
## 70   OTU_5355 0.001160379  100.00000   other_bacteria
## 71   OTU_5398 0.005423033   90.69767  Prochlorococcus
## 72   OTU_5403 0.002407593   90.69767   other_bacteria
## 73   OTU_5414 0.001204118  100.00000   other_bacteria
## 74    OTU_542 0.001498072   93.02326   other_bacteria
## 75   OTU_5428 0.001070970  100.00000   other_bacteria
## 76   OTU_5432 0.002228776   93.02326   other_bacteria
## 77   OTU_5441 0.002136152   93.02326   other_bacteria
## 78   OTU_5445 0.001281948  100.00000   other_bacteria
## 79   OTU_5447 0.002478991  100.00000   other_bacteria
## 80   OTU_5449 0.001256219   93.02326   other_bacteria
## 81   OTU_5491 0.001247857  100.00000   other_bacteria
## 82   OTU_5493 0.001173886   95.34884   other_bacteria
## 83   OTU_5499 0.001057463   93.02326   other_bacteria
## 84   OTU_5500 0.001371357  100.00000   other_bacteria
## 85   OTU_5511 0.001293526   93.02326   other_bacteria
## 86   OTU_5519 0.001240782   48.83721   other_bacteria
## 87   OTU_5523 0.001213123  100.00000   other_bacteria
## 88   OTU_5564 0.001316682   93.02326   other_bacteria
## 89   OTU_5586 0.001207334   95.34884   other_bacteria
## 90   OTU_5607 0.001467197   93.02326   other_bacteria
## 91   OTU_5624 0.001290953   95.34884   other_bacteria
## 92   OTU_5633 0.002238424   95.34884   other_bacteria
## 93   OTU_5635 0.002038381  100.00000   other_bacteria
## 94   OTU_5651 0.001368140   93.02326   other_bacteria
## 95   OTU_5653 0.001828047   93.02326   other_bacteria
## 96   OTU_5662 0.001409950   90.69767   other_bacteria
## 97   OTU_5665 0.001334693   93.02326   other_bacteria
## 98   OTU_5667 0.001355276   93.02326   other_bacteria
## 99   OTU_5691 0.001470413   93.02326   other_bacteria
## 100  OTU_5727 0.002715698   93.02326   other_bacteria
## 101  OTU_5741 0.001373929  100.00000   other_bacteria
## 102  OTU_5742 0.001326974   93.02326   other_bacteria
## 103  OTU_5752 0.001840911   90.69767  Prochlorococcus
## 104  OTU_5772 0.001898801  100.00000   other_bacteria
## 105  OTU_5786 0.001188681   83.72093    Synechococcus
## 106  OTU_5800 0.001009864   93.02326   other_bacteria
## 107  OTU_5804 0.001425387   93.02326   other_bacteria
## 108  OTU_5815 0.001025301  100.00000   other_bacteria
## 109  OTU_5817 0.001042025  100.00000   other_bacteria
## 110  OTU_5821 0.001091553   93.02326   other_bacteria
## 111  OTU_5823 0.001253003   93.02326   other_bacteria
## 112  OTU_5879 0.001743784   93.02326   other_bacteria
## 113  OTU_5880 0.001172600   90.69767   other_bacteria
## 114  OTU_5911 0.001307034  100.00000   other_bacteria
## 115  OTU_5925 0.001328260   86.04651   other_bacteria
## 116  OTU_5942 0.001259435  100.00000   other_bacteria
## 117  OTU_5961 0.001958621  100.00000   other_bacteria
## 118  OTU_5968 0.001397086  100.00000   other_bacteria
## 119  OTU_5976 0.001164881   93.02326   other_bacteria
## 120  OTU_5978 0.001993355  100.00000   other_bacteria
## 121  OTU_5982 0.001111493   93.02326   other_bacteria
## 122  OTU_5985 0.001362351  100.00000   other_bacteria
## 123  OTU_5988 0.001011150   93.02326   other_bacteria
## 124  OTU_6047 0.001099915  100.00000   other_bacteria
## 125  OTU_6067 0.001894942  100.00000   other_bacteria
## 126  OTU_6083 0.003165955   86.04651    Synechococcus
## 127  OTU_6102 0.001303175   93.02326   other_bacteria
## 128  OTU_6155 0.001512866  100.00000   other_bacteria
## 129  OTU_6164 0.002118784   93.02326   other_bacteria
## 130  OTU_6193 0.001176459  100.00000   other_bacteria
## 131   OTU_635 0.003025732   93.02326   other_bacteria
## 132   OTU_709 0.003061110   93.02326   other_bacteria
## 133  OTU_7407 0.001341125   90.69767   other_bacteria
## 134  OTU_7455 0.001168097  100.00000   other_bacteria
## 135   OTU_759 0.001018226   86.04651    Synechococcus
## 136   OTU_761 0.008529169   93.02326  Prochlorococcus
## 137   OTU_790 0.001005361  100.00000   other_bacteria
## 138  OTU_7987 0.001436966  100.00000   other_bacteria
## 139  OTU_8011 0.003102276   83.72093   other_bacteria
## 140  OTU_8146 0.001164238  100.00000   other_bacteria
## 141  OTU_8153 0.001957335   93.02326   other_bacteria
## 142  OTU_8163 0.002039668  100.00000   other_bacteria
## 143  OTU_8367 0.001419598  100.00000   other_bacteria
## 144  OTU_8377 0.001168741  100.00000   other_bacteria
## 145  OTU_8436 0.001075473  100.00000   other_bacteria
## 146  OTU_8458 0.001327617  100.00000   other_bacteria
## 147  OTU_9255 0.001645371   86.04651    Synechococcus
## 148  OTU_9267 0.001112780   83.72093    Synechococcus
## 149   OTU_934 0.001139795  100.00000   other_bacteria
## [1] 149   5

Proportion of regionally abundant OTUs (%):

## [1] 0.7539341

Cosmopolitan OTUs (relative abundance over 0.1% and occurence in more than 80% of samples):

otu_tb16_ss1154_cosmop_sorted_prov<-cbind(otu_names=row.names(otu_tb16_ss36155_cosmop_sorted),otu_tb16_ss36155_cosmop_sorted)
##     otu_names mean_rabund perc_occur          class_B
## 1    OTU_1329 0.002241640   93.02326   other_bacteria
## 2    OTU_1676 0.002044814   88.37209  Prochlorococcus
## 3    OTU_1738 0.001929676   93.02326   other_bacteria
## 4    OTU_1754 0.011149026   93.02326  Prochlorococcus
## 5    OTU_1942 0.006453480   93.02326  Prochlorococcus
## 6     OTU_223 0.001027231   93.02326   other_bacteria
## 7      OTU_23 0.001443398   93.02326   other_bacteria
## 8    OTU_2428 0.007645377   93.02326   other_bacteria
## 9    OTU_2466 0.006429681   93.02326  Prochlorococcus
## 10   OTU_2789 0.001014366  100.00000   other_bacteria
## 11  OTU_27900 0.002379934  100.00000 Prymnesiophyceae
## 12  OTU_27901 0.003573117   81.39535 Prymnesiophyceae
## 13  OTU_27934 0.001615139   95.34884 Prymnesiophyceae
## 14  OTU_27938 0.001353989   93.02326    Pelagophyceae
## 15   OTU_2866 0.003430321   90.69767   other_bacteria
## 16   OTU_2877 0.002066683   95.34884   other_bacteria
## 17   OTU_2893 0.008587059   93.02326   other_bacteria
## 18     OTU_29 0.002464840  100.00000   other_bacteria
## 19   OTU_2980 0.001006648  100.00000   other_bacteria
## 20   OTU_3004 0.002071829   93.02326   other_bacteria
## 21   OTU_3023 0.001958621   93.02326   other_bacteria
## 22   OTU_3162 0.002286023   95.34884   other_bacteria
## 23   OTU_3172 0.002888082   88.37209   other_bacteria
## 24   OTU_3173 0.001013080   83.72093   other_bacteria
## 25   OTU_3187 0.003630364  100.00000   other_bacteria
## 26   OTU_3197 0.001815825   81.39535   other_bacteria
## 27   OTU_3198 0.001436966   93.02326   other_bacteria
## 28   OTU_3207 0.001030447   90.69767   other_bacteria
## 29   OTU_3214 0.001204761   93.02326   other_bacteria
## 30   OTU_3240 0.001783021   93.02326   other_bacteria
## 31   OTU_3271 0.005586413   90.69767  Prochlorococcus
## 32   OTU_3308 0.002082121   97.67442    Synechococcus
## 33   OTU_3311 0.002843056   90.69767  Prochlorococcus
## 34   OTU_3326 0.001315396   90.69767   other_bacteria
## 35    OTU_333 0.001588123  100.00000   other_bacteria
## 36   OTU_3347 0.001297386   97.67442   other_bacteria
## 37   OTU_3680 0.001653732   93.02326   other_bacteria
## 38   OTU_3731 0.001496142  100.00000   other_bacteria
## 39   OTU_3736 0.007181611   93.02326  Prochlorococcus
## 40   OTU_3789 0.001064538  100.00000   other_bacteria
## 41   OTU_3803 0.001385507  100.00000   other_bacteria
## 42   OTU_3810 0.001757292   93.02326   other_bacteria
## 43   OTU_4036 0.001322471   97.67442   other_bacteria
## 44   OTU_4048 0.002347129  100.00000   other_bacteria
## 45   OTU_4083 0.001072257   95.34884   other_bacteria
## 46   OTU_4366 0.001663381  100.00000   other_bacteria
## 47   OTU_4560 0.001658878  100.00000   other_bacteria
## 48   OTU_4664 0.001741211  100.00000   other_bacteria
## 49   OTU_4926 0.001751503   93.02326   other_bacteria
## 50   OTU_4991 0.001551460   95.34884   other_bacteria
## 51    OTU_520 0.001058749   93.02326   other_bacteria
## 52   OTU_5211 0.001081262   95.34884   other_bacteria
## 53   OTU_5222 0.001090910   93.02326   other_bacteria
## 54   OTU_5266 0.001177102   93.02326   other_bacteria
## 55   OTU_5268 0.001193826  100.00000   other_bacteria
## 56   OTU_5288 0.001213123   90.69767  Prochlorococcus
## 57   OTU_5301 0.001794599   95.34884   other_bacteria
## 58   OTU_5327 0.001590696   93.02326   other_bacteria
## 59   OTU_5330 0.004964414   93.02326  Prochlorococcus
## 60   OTU_5355 0.001160379  100.00000   other_bacteria
## 61   OTU_5398 0.005423033   90.69767  Prochlorococcus
## 62   OTU_5403 0.002407593   90.69767   other_bacteria
## 63   OTU_5414 0.001204118  100.00000   other_bacteria
## 64    OTU_542 0.001498072   93.02326   other_bacteria
## 65   OTU_5428 0.001070970  100.00000   other_bacteria
## 66   OTU_5432 0.002228776   93.02326   other_bacteria
## 67   OTU_5441 0.002136152   93.02326   other_bacteria
## 68   OTU_5445 0.001281948  100.00000   other_bacteria
## 69   OTU_5447 0.002478991  100.00000   other_bacteria
## 70   OTU_5449 0.001256219   93.02326   other_bacteria
## 71   OTU_5491 0.001247857  100.00000   other_bacteria
## 72   OTU_5493 0.001173886   95.34884   other_bacteria
## 73   OTU_5499 0.001057463   93.02326   other_bacteria
## 74   OTU_5500 0.001371357  100.00000   other_bacteria
## 75   OTU_5511 0.001293526   93.02326   other_bacteria
## 76   OTU_5523 0.001213123  100.00000   other_bacteria
## 77   OTU_5564 0.001316682   93.02326   other_bacteria
## 78   OTU_5586 0.001207334   95.34884   other_bacteria
## 79   OTU_5607 0.001467197   93.02326   other_bacteria
## 80   OTU_5624 0.001290953   95.34884   other_bacteria
## 81   OTU_5633 0.002238424   95.34884   other_bacteria
## 82   OTU_5635 0.002038381  100.00000   other_bacteria
## 83   OTU_5651 0.001368140   93.02326   other_bacteria
## 84   OTU_5653 0.001828047   93.02326   other_bacteria
## 85   OTU_5662 0.001409950   90.69767   other_bacteria
## 86   OTU_5665 0.001334693   93.02326   other_bacteria
## 87   OTU_5667 0.001355276   93.02326   other_bacteria
## 88   OTU_5691 0.001470413   93.02326   other_bacteria
## 89   OTU_5727 0.002715698   93.02326   other_bacteria
## 90   OTU_5741 0.001373929  100.00000   other_bacteria
## 91   OTU_5742 0.001326974   93.02326   other_bacteria
## 92   OTU_5752 0.001840911   90.69767  Prochlorococcus
## 93   OTU_5772 0.001898801  100.00000   other_bacteria
## 94   OTU_5786 0.001188681   83.72093    Synechococcus
## 95   OTU_5800 0.001009864   93.02326   other_bacteria
## 96   OTU_5804 0.001425387   93.02326   other_bacteria
## 97   OTU_5815 0.001025301  100.00000   other_bacteria
## 98   OTU_5817 0.001042025  100.00000   other_bacteria
## 99   OTU_5821 0.001091553   93.02326   other_bacteria
## 100  OTU_5823 0.001253003   93.02326   other_bacteria
## 101  OTU_5879 0.001743784   93.02326   other_bacteria
## 102  OTU_5880 0.001172600   90.69767   other_bacteria
## 103  OTU_5911 0.001307034  100.00000   other_bacteria
## 104  OTU_5925 0.001328260   86.04651   other_bacteria
## 105  OTU_5942 0.001259435  100.00000   other_bacteria
## 106  OTU_5961 0.001958621  100.00000   other_bacteria
## 107  OTU_5968 0.001397086  100.00000   other_bacteria
## 108  OTU_5976 0.001164881   93.02326   other_bacteria
## 109  OTU_5978 0.001993355  100.00000   other_bacteria
## 110  OTU_5982 0.001111493   93.02326   other_bacteria
## 111  OTU_5985 0.001362351  100.00000   other_bacteria
## 112  OTU_5988 0.001011150   93.02326   other_bacteria
## 113  OTU_6047 0.001099915  100.00000   other_bacteria
## 114  OTU_6067 0.001894942  100.00000   other_bacteria
## 115  OTU_6083 0.003165955   86.04651    Synechococcus
## 116  OTU_6102 0.001303175   93.02326   other_bacteria
## 117  OTU_6155 0.001512866  100.00000   other_bacteria
## 118  OTU_6164 0.002118784   93.02326   other_bacteria
## 119  OTU_6193 0.001176459  100.00000   other_bacteria
## 120   OTU_635 0.003025732   93.02326   other_bacteria
## 121   OTU_709 0.003061110   93.02326   other_bacteria
## 122  OTU_7407 0.001341125   90.69767   other_bacteria
## 123  OTU_7455 0.001168097  100.00000   other_bacteria
## 124   OTU_759 0.001018226   86.04651    Synechococcus
## 125   OTU_761 0.008529169   93.02326  Prochlorococcus
## 126   OTU_790 0.001005361  100.00000   other_bacteria
## 127  OTU_7987 0.001436966  100.00000   other_bacteria
## 128  OTU_8011 0.003102276   83.72093   other_bacteria
## 129  OTU_8146 0.001164238  100.00000   other_bacteria
## 130  OTU_8153 0.001957335   93.02326   other_bacteria
## 131  OTU_8163 0.002039668  100.00000   other_bacteria
## 132  OTU_8367 0.001419598  100.00000   other_bacteria
## 133  OTU_8377 0.001168741  100.00000   other_bacteria
## 134  OTU_8436 0.001075473  100.00000   other_bacteria
## 135  OTU_8458 0.001327617  100.00000   other_bacteria
## 136  OTU_9255 0.001645371   86.04651    Synechococcus
## 137  OTU_9267 0.001112780   83.72093    Synechococcus
## 138   OTU_934 0.001139795  100.00000   other_bacteria
## [1] 138   5

Number and proportion (%) of cosmopolitan OTUs:

## [1] 138
## [1] 0.6982746

Number and proportion (%) of rare OTUs:

## [1] 13963
## [1] 70.65223

2.6) Taxonomic composition analysis

2.6.1) Normalized data

2.6.1.1) Absolute values

Let’s add the taxonomic classification by merging “tb16_tax_occur_ss36155_no_cero” with “tb16_tax”:

tb16_bacteria <- tb16_ss36155_tax_sorted[which(tb16_ss36155_tax_sorted$class_A == "other_bacteria" | tb16_ss36155_tax_sorted$class_A == "Cyanobacteria" ),]

tb16_protists <- tb16_ss36155_tax_sorted[which(tb16_ss36155_tax_sorted$class_A != "other_bacteria" &  tb16_ss36155_tax_sorted$class_A != "Cyanobacteria"),]

dim(tb16_protists)
## [1] 318  47
dim(tb16_bacteria)
## [1] 19445    47
#tb16_protists[1:5,43:47]
#tb16_bacteria[1:5,43:47]
#create a table per group and count in how many samples they occur. 
Dinophyceae_tb <- tb16_protists[which(tb16_protists$class_A == "Dinophyceae"),]
Dinophyceae_tb[1:5,1:5]
##           MP0311 MP1517 MP1672 MP2821 TARA_102_SUR_0d2_3
## OTU_27905      0      0      0      0                  0
## OTU_27950      0      0      0      0                  0
## OTU_28007      1      0      0      0                  0
## OTU_28206      0      0      0      0                  0
## OTU_28215      0      0      0      0                  0
Dinophyceae_tb_occur <- Dinophyceae_tb[,1:43]
Dinophyceae_tb_occur[1:5,1:5]
##           MP0311 MP1517 MP1672 MP2821 TARA_102_SUR_0d2_3
## OTU_27905      0      0      0      0                  0
## OTU_27950      0      0      0      0                  0
## OTU_28007      1      0      0      0                  0
## OTU_28206      0      0      0      0                  0
## OTU_28215      0      0      0      0                  0
dim(Dinophyceae_tb_occur)
## [1]  5 43
length(Dinophyceae_tb_occur[,colSums(Dinophyceae_tb_occur) > 0])
## [1] 7
#Dinophyceae_tb_samples <- Dinophyceae_tb_occur[,colSums(Dinophyceae_tb_occur) > 0]
#length(Dinophyceae_tb_samples[which(colSums(Dinophyceae_tb_occur) != 0)])

Prasinophyceae_tb <- tb16_protists[which(tb16_protists$class_A == "other_Prasinophyceae"),]
Prasinophyceae_tb_occur <- Prasinophyceae_tb[,1:43]
length(Prasinophyceae_tb_occur[,colSums(Prasinophyceae_tb_occur) > 0])
## [1] 39
Chrysophyceae_tb <- tb16_protists[which(tb16_protists$class_A == "Chrysophyceae"),]
Chrysophyceae_tb_occur <- Chrysophyceae_tb[,1:43]
length(Chrysophyceae_tb_occur[,colSums(Chrysophyceae_tb_occur) > 0])
## [1] 0
Pelagophyceae_tb <- tb16_protists[which(tb16_protists$class_A == "Pelagophyceae"),]
Pelagophyceae_tb_occur <- Pelagophyceae_tb[,1:43]
length(Pelagophyceae_tb_occur[,colSums(Pelagophyceae_tb_occur) > 0])
## [1] 43
Dictyochophyceae_tb <- tb16_protists[which(tb16_protists$class_A == "Dictyochophyceae"),]
Dictyochophyceae_tb_occur <- Dictyochophyceae_tb[,1:43]
length(Dictyochophyceae_tb_occur[,colSums(Dictyochophyceae_tb_occur) > 0])
## [1] 42
Cryptomonadales_tb <- tb16_protists[which(tb16_protists$class_A == "Cryptophyceae"),]
Cryptomonadales_tb_occur <- Cryptomonadales_tb[,1:43]
length(Cryptomonadales_tb_occur[,colSums(Cryptomonadales_tb_occur) > 0])
## [1] 29
Bacillariophyta_tb <- tb16_protists[which(tb16_protists$class_A == "Bacillariophyceae"),]
Bacillariophyta_tb_occur <- Bacillariophyta_tb[,1:43]
length(Bacillariophyta_tb_occur[,colSums(Bacillariophyta_tb_occur) > 0])
## [1] 35
Chlorarachniophyta_tb <- tb16_protists[which(tb16_protists$class_A == "Chlorarachniophyceae"),]
Chlorarachniophyta_tb_occur <- Chlorarachniophyta_tb[,1:43]
length(Chlorarachniophyta_tb_occur[,colSums(Chlorarachniophyta_tb_occur) > 0])
## [1] 5
Bolidophyceae_tb <- tb16_protists[which(tb16_protists$class_A == "Bolidophyceae"),]
Bolidophyceae_tb_occur <- Bolidophyceae_tb[,1:43]
length(Bolidophyceae_tb_occur[,colSums(Bolidophyceae_tb_occur) > 0])
## [1] 29
Pinguiochysidales_tb <- tb16_protists[which(tb16_protists$class_A == "Pinguiophyceae"),]
Pinguiochysidales_tb_occur <- Pinguiochysidales_tb[,1:43]
length(Pinguiochysidales_tb_occur[,colSums(Pinguiochysidales_tb_occur) > 0])
## [1] 2
Prymnesiophyceae_tb <- tb16_protists[which(tb16_protists$class_A == "Prymnesiophyceae"),]
Prymnesiophyceae_tb_occur <- Prymnesiophyceae_tb[,1:43]
length(Prymnesiophyceae_tb_occur[,colSums(Prymnesiophyceae_tb_occur) > 0])
## [1] 43
Mamiellophyceae_tb <- tb16_protists[which(tb16_protists$class_A == "Mamiellophyceae"),]
Mamiellophyceae_tb_occur <- Mamiellophyceae_tb[,1:43]
length(Mamiellophyceae_tb_occur[,colSums(Mamiellophyceae_tb_occur) > 0])
## [1] 30
Eustigmatophyceae_tb <- tb16_protists[which(tb16_protists$class_A == "Eustigmatophyceae"),]
Eustigmatophyceae_tb_occur <- Eustigmatophyceae_tb[,1:43]
length(Eustigmatophyceae_tb_occur[,colSums(Eustigmatophyceae_tb_occur) > 0])
## [1] 7
Chlorophyceae_tb <- tb16_protists[which(tb16_protists$class_A == "Chlorophyceae"),]
Chlorophyceae_tb_occur <- Chlorophyceae_tb[,1:43]
length(Chlorophyceae_tb_occur[,colSums(Chlorophyceae_tb_occur) > 0])
## [1] 1
Ulvophyceae_tb <- tb16_protists[which(tb16_protists$class_A == "Ulvophyceae"),]
Ulvophyceae_tb_occur <- Ulvophyceae_tb[,1:43]
length(Ulvophyceae_tb_occur[,colSums(Ulvophyceae_tb_occur) > 0])
## [1] 0
Raphydophyceae_tb <- tb16_protists[which(tb16_protists$class_A == "Raphydophyceae"),]
Raphydophyceae_tb_occur <- Raphydophyceae_tb[,1:43]
length(Raphydophyceae_tb_occur[,colSums(Raphydophyceae_tb_occur) > 0])
## [1] 0
Trebouxiophyceae_tb <- tb16_protists[which(tb16_protists$class_A == "Trebouxiophyceae"),]
Trebouxiophyceae_tb_occur <- Trebouxiophyceae_tb[,1:43]
length(Trebouxiophyceae_tb_occur[,colSums(Trebouxiophyceae_tb_occur) > 0])
## [1] 1
Phaeophyceae_tb <- tb16_protists[which(tb16_protists$class_A == "Phaeophyceae"),]
Phaeophyceae_tb_occur <- Phaeophyceae_tb[,1:43]
length(Phaeophyceae_tb_occur[,colSums(Phaeophyceae_tb_occur) > 0])
## [1] 2
Phaeothamniophyceae_tb <- tb16_protists[which(tb16_protists$class_A == "Phaeothamniophyceae"),]
Phaeothamniophyceae_tb_occur <- Phaeothamniophyceae_tb[,1:43]
length(Phaeothamniophyceae_tb_occur[,colSums(Phaeothamniophyceae_tb_occur) > 0])
## [1] 0
Xanthophyceae_tb <- tb16_protists[which(tb16_protists$class_A == "Xanthophyceae"),]
Xanthophyceae_tb_occur <- Xanthophyceae_tb[,1:43]
length(Xanthophyceae_tb_occur[,colSums(Xanthophyceae_tb_occur) > 0])
## [1] 0
Chlorodendrophyceae_tb <- tb16_protists[which(tb16_protists$class_A == "Chlorodendrophyceae"),]
Chlorodendrophyceae_tb_occur <- Chlorodendrophyceae_tb[,1:43]
length(Chlorodendrophyceae_tb_occur[,colSums(Chlorodendrophyceae_tb_occur) > 0])
## [1] 1
IncertaeSedis_Archaeplastida_tb <- tb16_protists[which(tb16_protists$class_A == "IncertaeSedis_Archaeplastida"),]
IncertaeSedis_Archaeplastida_tb_occur <- IncertaeSedis_Archaeplastida_tb[,1:43]
length(IncertaeSedis_Archaeplastida_tb_occur[,colSums(IncertaeSedis_Archaeplastida_tb_occur) > 0])
## [1] 0
Nephroselmidophyceae_tb <- tb16_protists[which(tb16_protists$class_A == "Nephroselmidophyceae"),]
Nephroselmidophyceae_tb_occur <- Nephroselmidophyceae_tb[,1:43]
length(Nephroselmidophyceae_tb_occur[,colSums(Nephroselmidophyceae_tb_occur) > 0])
## [1] 0
Pavlovophyceae_tb <- tb16_protists[which(tb16_protists$class_A == "Pavlovophyceae"),]
Pavlovophyceae_tb_occur <- Pavlovophyceae_tb[,1:43]
length(Pavlovophyceae_tb_occur[,colSums(Pavlovophyceae_tb_occur) > 0])
## [1] 2
Rhodophyceae_tb <- tb16_protists[which(tb16_protists$class_A == "Rhodophyceae"),]
Rhodophyceae_tb_occur <- Rhodophyceae_tb[,1:43]
length(Rhodophyceae_tb_occur[,colSums(Rhodophyceae_tb_occur) > 0])
## [1] 0
Rappemonads_tb <- tb16_protists[which(tb16_protists$class_A == "Rappemonads"),]
Rappemonads_tb_occur <- Rappemonads_tb[,1:43]
length(Rappemonads_tb_occur[,colSums(Rappemonads_tb_occur) > 0])
## [1] 25
MOCH_1_tb <- tb16_protists[which(tb16_protists$class_A == "MOCH-1"),]
MOCH_1_tb_occur <- MOCH_1_tb[,1:43]
length(MOCH_1_tb_occur[,colSums(MOCH_1_tb_occur) > 0])
## [1] 0
MOCH_2_tb <- tb16_protists[which(tb16_protists$class_A == "MOCH-2"),]
MOCH_2_tb_occur <- MOCH_2_tb[,1:43]
length(MOCH_2_tb_occur[,colSums(MOCH_2_tb_occur) > 0])
## [1] 0
MOCH_5_tb <- tb16_protists[which(tb16_protists$class_A == "MOCH-5"),]
MOCH_5_tb_occur <- MOCH_5_tb[,1:43]
length(MOCH_5_tb_occur[,colSums(MOCH_5_tb_occur) > 0])
## [1] 0
Prasinophyceae_clade_VII_tb <- tb16_protists[which(tb16_protists$class_A == "Prasinophyceae_clade-VII"),]
Prasinophyceae_clade_VII_tb_occur <- Prasinophyceae_clade_VII_tb[,1:43]
length(Prasinophyceae_clade_VII_tb_occur[,colSums(Prasinophyceae_clade_VII_tb_occur) > 0])
## [1] 0
Prasinophyceae_clade_IX_tb <- tb16_protists[which(tb16_protists$class_A == "Prasinophyceae_clade-IX"),]
Prasinophyceae_clade_IX_tb_occur <- Prasinophyceae_clade_IX_tb[,1:43]
length(Prasinophyceae_clade_IX_tb_occur[,colSums(Prasinophyceae_clade_IX_tb_occur) > 0])
## [1] 0
Pyramimonadaceae_tb <- tb16_protists[which(tb16_protists$class_A == "Pyramimonadaceae"),]
Pyramimonadaceae_tb_occur <- Pyramimonadaceae_tb[,1:43]
length(Pyramimonadaceae_tb_occur[,colSums(Pyramimonadaceae_tb_occur) > 0])
## [1] 6
other_plastids_tb <- tb16_protists[which(tb16_protists$class_A == "other_plastids"),]
other_plastids_tb_occur <- other_plastids_tb[,1:43]
length(other_plastids_tb_occur[,colSums(other_plastids_tb_occur) > 0])
## [1] 21
#create a table per group and count in how many samples they occur. 
heterotrophic_bacteria_tb <- tb16_bacteria[which(tb16_bacteria$class_A == "other_bacteria"),]
heterotrophic_bacteria_tb_occur <- heterotrophic_bacteria_tb[,1:43]
length(heterotrophic_bacteria_tb_occur[,colSums(heterotrophic_bacteria_tb_occur) > 0])

Cyanobacteria_tb <- tb16_bacteria[which(tb16_bacteria$class_A == "Cyanobacteria"),]
Cyanobacteria_tb_occur <- Cyanobacteria_tb[,1:43]
length(Cyanobacteria_tb_occur[,colSums(Cyanobacteria_tb_occur) > 0])
##                      reads_per_class OTUs_per_class
## Bacillariophyceae                725            136
## Bolidophyceae                    158              5
## Chlorarachniophyceae              12              4
## Chlorodendrophyceae                1              1
## Chlorophyceae                      1              1
## Cryptophyceae                   1801             26
## Dictyochophyceae                1219              7
## Dinophyceae                       14              5
## Eustigmatophyceae                 15              2
## Mamiellophyceae                15689             14
## Pavlovophyceae                     2              1
## Pelagophyceae                   5578             10
## Phaeophyceae                       2              2
## Pinguiophyceae                     2              1
## Prymnesiophyceae               25911             50
## Pyramimonadaceae                  79              5
## Rappemonads                      121              4
## Trebouxiophyceae                   1              1
## other_Prasinophyceae            1183             21
## other_plastids                    53             22
##                      reads_per_class OTUs_per_class samples_per_class
## Prymnesiophyceae               25911             50                43
## Mamiellophyceae                15689             14                30
## Pelagophyceae                   5578             10                43
## Cryptophyceae                   1801             26                29
## Dictyochophyceae                1219              7                42
## other_Prasinophyceae            1183             21                39
## Bacillariophyceae                725            136                35
## Bolidophyceae                    158              5                29
## Rappemonads                      121              4                25
## Pyramimonadaceae                  79              5                 6
## other_plastids                    53             22                21
## Eustigmatophyceae                 15              2                 7
## Dinophyceae                       14              5                 7
## Chlorarachniophyceae              12              4                 5
## Phaeophyceae                       2              2                 2
## Pavlovophyceae                     2              1                 2
## Pinguiophyceae                     2              1                 2
## Chlorodendrophyceae                1              1                 1
## Chlorophyceae                      1              1                 1
## Trebouxiophyceae                   1              1                 1
##                      reads_per_class OTUs_per_class samples_per_class
## Prymnesiophyceae               25911             50                43
## Mamiellophyceae                15689             14                30
## Pelagophyceae                   5578             10                43
## Cryptophyceae                   1801             26                29
## Dictyochophyceae                1219              7                42
## other_Prasinophyceae            1183             21                39
## Bacillariophyceae                725            136                35
## Bolidophyceae                    158              5                29
## Rappemonads                      121              4                25
## Pyramimonadaceae                  79              5                 6
## Eustigmatophyceae                 15              2                 7
## Dinophyceae                       14              5                 7
## Chlorarachniophyceae              12              4                 5
## Phaeophyceae                       2              2                 2
## Pavlovophyceae                     2              1                 2
## Pinguiophyceae                     2              1                 2
## Chlorodendrophyceae                1              1                 1
## Chlorophyceae                      1              1                 1
## Trebouxiophyceae                   1              1                 1
##                reads_per_class OTUs_per_class
## Cyanobacteria           171416            344
## other_bacteria         1330682          19101
## NA                          NA             NA
## NA.1                        NA             NA
## NA.2                        NA             NA
##                reads_per_class OTUs_per_class samples_per_class
## other_bacteria         1330682          19101                43
## Cyanobacteria           171416            344                43
cyano_tb <- tb16_bacteria[which(tb16_bacteria$class_A != "other_bacteria"),]

class_summary_reads_per_class_cyano<-aggregate(rowSums(cyano_tb[1:43]), list(cyano_tb$class_B), sum)
# count the different groups
class_summary_otus_per_class_cyano<-aggregate(rowSums(cyano_tb[1:43]), list(cyano_tb$class_B), length)

## READS PER CLASS ##
attach(class_summary_reads_per_class_cyano)
class_summary_reads_per_class_cyano_order<-class_summary_reads_per_class_cyano[order(-x),]
detach(class_summary_reads_per_class_cyano)
class_summary_reads_per_class_cyano_order
##               Group.1      x
## 1     Prochlorococcus 125651
## 2       Synechococcus  41990
## 3 other_cyanobacteria   3775
#fix column names
row.names(class_summary_reads_per_class_cyano_order)<-class_summary_reads_per_class_cyano_order[,1]
class_summary_reads_per_class_cyano_order<-class_summary_reads_per_class_cyano_order[c(-1)]
colnames(class_summary_reads_per_class_cyano_order)<-c("reads_per_class")


## OTUs PER CLASS ##
attach(class_summary_otus_per_class_cyano)
class_summary_otus_per_class_cyano_order<-class_summary_otus_per_class_cyano[order(-x),]
detach(class_summary_otus_per_class_cyano)
class_summary_otus_per_class_cyano_order
##               Group.1   x
## 3 other_cyanobacteria 143
## 2       Synechococcus 102
## 1     Prochlorococcus  99
row.names(class_summary_otus_per_class_cyano_order)<-class_summary_otus_per_class_cyano_order[,1]
class_summary_otus_per_class_cyano_order<-class_summary_otus_per_class_cyano_order[c(-1)]
colnames(class_summary_otus_per_class_cyano_order)<-c("OTUs_per_class")

# create_table_merging_#OTUs_#reads
cyano_OTUs_reads <- merge(class_summary_reads_per_class_cyano_order, class_summary_otus_per_class_cyano_order, by="row.names")

row.names(cyano_OTUs_reads)<-cyano_OTUs_reads[,1]
cyano_OTUs_reads<-cyano_OTUs_reads[,-1]
colnames(cyano_OTUs_reads)<-c("reads_per_class","OTUs_per_class")
cyano_OTUs_reads[1:3,1:2]
##                     reads_per_class OTUs_per_class
## Prochlorococcus              125651             99
## Synechococcus                 41990            102
## other_cyanobacteria            3775            143
cyano_OTUs_reads<-cyano_OTUs_reads[order(cyano_OTUs_reads$reads_per_class, cyano_OTUs_reads$OTUs_per_class, decreasing = T), c(1,2)]
cyano_OTUs_reads
##                     reads_per_class OTUs_per_class
## Prochlorococcus              125651             99
## Synechococcus                 41990            102
## other_cyanobacteria            3775            143
#compute relative values
cyano_OTUs_reads_rel_abund <- cyano_OTUs_reads

cyano_OTUs_reads_rel_abund$reads_per_class<-(cyano_OTUs_reads_rel_abund$reads_per_class*100)/colSums(cyano_OTUs_reads)[1]
cyano_OTUs_reads_rel_abund$OTUs_per_class<-(cyano_OTUs_reads_rel_abund$OTUs_per_class*100)/colSums(cyano_OTUs_reads)[2]

colSums(cyano_OTUs_reads_rel_abund)
## reads_per_class  OTUs_per_class 
##             100             100
rownames(cyano_OTUs_reads_rel_abund) = c("Prochlorococcus", "Synechococcus", "Other cyanobacteria")
cyano_OTUs_reads_rel_abund
##                     reads_per_class OTUs_per_class
## Prochlorococcus           73.301792       28.77907
## Synechococcus             24.495963       29.65116
## Other cyanobacteria        2.202245       41.56977
cyano_OTUs_reads_rel_abund["cyano_group"]<-NA
cyano_OTUs_reads_rel_abund$cyano_group<-c("Prochlorococcus", "Synechococcus", "Other cyanobacteria")

cyano_OTUs_reads_rel_abund2<-read.table("input/cyano_histograms_data.txt", head=TRUE)
cyano_OTUs_reads_rel_abund2
##                 group     value       data
## 1     Prochlorococcus 73.479888 % of reads
## 2     Prochlorococcus 28.323700  % of OTUs
## 3       Synechococcus 24.288471 % of reads
## 4       Synechococcus 30.346820  % of OTUs
## 5 other_cyanobacteria  2.231642 % of reads
## 6 other_cyanobacteria 41.329480  % of OTUs
ggplot(cyano_OTUs_reads_rel_abund2, aes(x=group, y=value, fill=data)) + 
  geom_bar(position="dodge", stat="identity") +
  scale_y_continuous(limits=c(-1,100), breaks=c(25,50,75,100)) +
  scale_fill_manual(values=c("#000000", "cadetblue3")) +
  labs(x="", y="% \n") + 
  theme(axis.text=element_text(size=14), axis.title=element_text(size=16)) + 
  theme(legend.title = element_blank(), legend.position=c(0.85,0.85), legend.text=element_text(size=14)) +
  theme(axis.title.y = element_text(size = rel(1.5), angle = 0, vjust=0.97))

2.6.1.2) Relative values

##   reads_per_class    OTUs_per_class samples_per_class 
##          100.0000          100.0000          911.6279
##                      reads_per_class OTUs_per_class samples_per_class
## Prymnesiophyceae        1.157103e+01        7.81250        100.000000
## Mamiellophyceae         7.006207e+00        2.18750         69.767442
## Pelagophyceae           2.490957e+00        1.56250        100.000000
## Cryptophyceae           8.042692e-01        4.06250         67.441860
## Dictyochophyceae        5.443665e-01        1.09375         97.674419
## other_Prasinophyceae    5.282901e-01        3.28125         90.697674
## Bacillariophyceae       3.237619e-01       21.25000         81.395349
## Bolidophyceae           7.055776e-02        0.78125         67.441860
## Rappemonads             5.403474e-02        0.62500         58.139535
## Pyramimonadaceae        3.527888e-02        0.78125         13.953488
## Eustigmatophyceae       6.698522e-03        0.31250         16.279070
## Dinophyceae             6.251954e-03        0.78125         16.279070
## Chlorarachniophyceae    5.358817e-03        0.62500         11.627907
## Phaeophyceae            8.931362e-04        0.31250          4.651163
## Pavlovophyceae          8.931362e-04        0.15625          4.651163
## Pinguiophyceae          8.931362e-04        0.15625          4.651163
## Chlorodendrophyceae     4.465681e-04        0.15625          2.325581
## Chlorophyceae           4.465681e-04        0.15625          2.325581
## Trebouxiophyceae        4.465681e-04        0.15625          2.325581
## Cyanobacteria           7.654892e+01       53.75000        100.000000



Reads per class vs. OTUs per class:



Reads per class vs. samples in which they occurr:

2.6.2) Non-rarefied data

Let’s add the taxonomic classification by merging “tb16_tax_occur_min36155_t” with “tb16_tax”:

Selection of phototrophs:

## [1]  0 47
## [1] 318  47
## [1] 19445    47
#create a table per group and count in how many samples they occur. 
Dinophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Dinophyceae"),]
Dinophyceae_tb[1:5,1:5]
##           TARA_102_SUR_0d2_3 TARA_109_SUR_0d2_3 TARA_110_SUR_0d2_3
## OTU_27905                  0                  0                  0
## OTU_27950                  0                  0                  0
## OTU_28007                  0                  0                  0
## OTU_28206                  0                  1                  0
## OTU_28215                  0                  0                  0
##           TARA_111_SUR_0d2_3 TARA_112_SUR_0d2_3
## OTU_27905                  0                  1
## OTU_27950                  0                  0
## OTU_28007                  0                  0
## OTU_28206                  0                  0
## OTU_28215                  0                  0
Dinophyceae_tb_occur <- Dinophyceae_tb[,1:43]
Dinophyceae_tb_occur[1:5,1:5]
##           TARA_102_SUR_0d2_3 TARA_109_SUR_0d2_3 TARA_110_SUR_0d2_3
## OTU_27905                  0                  0                  0
## OTU_27950                  0                  0                  0
## OTU_28007                  0                  0                  0
## OTU_28206                  0                  1                  0
## OTU_28215                  0                  0                  0
##           TARA_111_SUR_0d2_3 TARA_112_SUR_0d2_3
## OTU_27905                  0                  1
## OTU_27950                  0                  0
## OTU_28007                  0                  0
## OTU_28206                  0                  0
## OTU_28215                  0                  0
dim(Dinophyceae_tb_occur)
## [1]  6 43
length(Dinophyceae_tb_occur[,colSums(Dinophyceae_tb_occur) > 0])
## [1] 11
#Dinophyceae_tb_samples <- Dinophyceae_tb_occur[,colSums(Dinophyceae_tb_occur) > 0]
#length(Dinophyceae_tb_samples[which(colSums(Dinophyceae_tb_occur) != 0)])

Prasinophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "other_Prasinophyceae"),]
Prasinophyceae_tb_occur <- Prasinophyceae_tb[,1:43]
length(Prasinophyceae_tb_occur[,colSums(Prasinophyceae_tb_occur) > 0])
## [1] 41
Chrysophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Chrysophyceae"),]
Chrysophyceae_tb_occur <- Chrysophyceae_tb[,1:43]
length(Chrysophyceae_tb_occur[,colSums(Chrysophyceae_tb_occur) > 0])
## [1] 0
Pelagophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Pelagophyceae"),]
Pelagophyceae_tb_occur <- Pelagophyceae_tb[,1:43]
length(Pelagophyceae_tb_occur[,colSums(Pelagophyceae_tb_occur) > 0])
## [1] 43
Dictyochophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Dictyochophyceae"),]
Dictyochophyceae_tb_occur <- Dictyochophyceae_tb[,1:43]
length(Dictyochophyceae_tb_occur[,colSums(Dictyochophyceae_tb_occur) > 0])
## [1] 43
Cryptomonadales_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Cryptophyceae"),]
Cryptomonadales_tb_occur <- Cryptomonadales_tb[,1:43]
length(Cryptomonadales_tb_occur[,colSums(Cryptomonadales_tb_occur) > 0])
## [1] 31
Bacillariophyta_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Bacillariophyceae"),]
Bacillariophyta_tb_occur <- Bacillariophyta_tb[,1:43]
length(Bacillariophyta_tb_occur[,colSums(Bacillariophyta_tb_occur) > 0])
## [1] 39
Chlorarachniophyta_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Chlorarachniophyceae"),]
Chlorarachniophyta_tb_occur <- Chlorarachniophyta_tb[,1:43]
length(Chlorarachniophyta_tb_occur[,colSums(Chlorarachniophyta_tb_occur) > 0])
## [1] 8
Bolidophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Bolidophyceae"),]
Bolidophyceae_tb_occur <- Bolidophyceae_tb[,1:43]
length(Bolidophyceae_tb_occur[,colSums(Bolidophyceae_tb_occur) > 0])
## [1] 34
Pinguiochysidales_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Pinguiophyceae"),]
Pinguiochysidales_tb_occur <- Pinguiochysidales_tb[,1:43]
length(Pinguiochysidales_tb_occur[,colSums(Pinguiochysidales_tb_occur) > 0])
## [1] 3
Prymnesiophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Prymnesiophyceae"),]
Prymnesiophyceae_tb_occur <- Prymnesiophyceae_tb[,1:43]
length(Prymnesiophyceae_tb_occur[,colSums(Prymnesiophyceae_tb_occur) > 0])
## [1] 43
Mamiellophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Mamiellophyceae"),]
Mamiellophyceae_tb_occur <- Mamiellophyceae_tb[,1:43]
length(Mamiellophyceae_tb_occur[,colSums(Mamiellophyceae_tb_occur) > 0])
## [1] 31
Eustigmatophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Eustigmatophyceae"),]
Eustigmatophyceae_tb_occur <- Eustigmatophyceae_tb[,1:43]
length(Eustigmatophyceae_tb_occur[,colSums(Eustigmatophyceae_tb_occur) > 0])
## [1] 9
Chlorophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Chlorophyceae"),]
Chlorophyceae_tb_occur <- Chlorophyceae_tb[,1:43]
length(Chlorophyceae_tb_occur[,colSums(Chlorophyceae_tb_occur) > 0])
## [1] 2
Ulvophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Ulvophyceae"),]
Ulvophyceae_tb_occur <- Ulvophyceae_tb[,1:43]
length(Ulvophyceae_tb_occur[,colSums(Ulvophyceae_tb_occur) > 0])
## [1] 0
Raphydophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Raphydophyceae"),]
Raphydophyceae_tb_occur <- Raphydophyceae_tb[,1:43]
length(Raphydophyceae_tb_occur[,colSums(Raphydophyceae_tb_occur) > 0])
## [1] 0
Trebouxiophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Trebouxiophyceae"),]
Trebouxiophyceae_tb_occur <- Trebouxiophyceae_tb[,1:43]
length(Trebouxiophyceae_tb_occur[,colSums(Trebouxiophyceae_tb_occur) > 0])
## [1] 1
Phaeophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Phaeophyceae"),]
Phaeophyceae_tb_occur <- Phaeophyceae_tb[,1:43]
length(Phaeophyceae_tb_occur[,colSums(Phaeophyceae_tb_occur) > 0])
## [1] 2
Phaeothamniophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Phaeothamniophyceae"),]
Phaeothamniophyceae_tb_occur <- Phaeothamniophyceae_tb[,1:43]
length(Phaeothamniophyceae_tb_occur[,colSums(Phaeothamniophyceae_tb_occur) > 0])
## [1] 0
Xanthophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Xanthophyceae"),]
Xanthophyceae_tb_occur <- Xanthophyceae_tb[,1:43]
length(Xanthophyceae_tb_occur[,colSums(Xanthophyceae_tb_occur) > 0])
## [1] 0
Chlorodendrophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Chlorodendrophyceae"),]
Chlorodendrophyceae_tb_occur <- Chlorodendrophyceae_tb[,1:43]
length(Chlorodendrophyceae_tb_occur[,colSums(Chlorodendrophyceae_tb_occur) > 0])
## [1] 2
IncertaeSedis_Archaeplastida_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "IncertaeSedis_Archaeplastida"),]
IncertaeSedis_Archaeplastida_tb_occur <- IncertaeSedis_Archaeplastida_tb[,1:43]
length(IncertaeSedis_Archaeplastida_tb_occur[,colSums(IncertaeSedis_Archaeplastida_tb_occur) > 0])
## [1] 0
Nephroselmidophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Nephroselmidophyceae"),]
Nephroselmidophyceae_tb_occur <- Nephroselmidophyceae_tb[,1:43]
length(Nephroselmidophyceae_tb_occur[,colSums(Nephroselmidophyceae_tb_occur) > 0])
## [1] 0
Pavlovophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Pavlovophyceae"),]
Pavlovophyceae_tb_occur <- Pavlovophyceae_tb[,1:43]
length(Pavlovophyceae_tb_occur[,colSums(Pavlovophyceae_tb_occur) > 0])
## [1] 2
Rhodophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Rhodophyceae"),]
Rhodophyceae_tb_occur <- Rhodophyceae_tb[,1:43]
length(Rhodophyceae_tb_occur[,colSums(Rhodophyceae_tb_occur) > 0])
## [1] 0
Rappemonads_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Rappemonads"),]
Rappemonads_tb_occur <- Rappemonads_tb[,1:43]
length(Rappemonads_tb_occur[,colSums(Rappemonads_tb_occur) > 0])
## [1] 37
MOCH_1_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "MOCH-1"),]
MOCH_1_tb_occur <- MOCH_1_tb[,1:43]
length(MOCH_1_tb_occur[,colSums(MOCH_1_tb_occur) > 0])
## [1] 0
MOCH_2_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "MOCH-2"),]
MOCH_2_tb_occur <- MOCH_2_tb[,1:43]
length(MOCH_2_tb_occur[,colSums(MOCH_2_tb_occur) > 0])
## [1] 0
MOCH_5_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "MOCH-5"),]
MOCH_5_tb_occur <- MOCH_5_tb[,1:43]
length(MOCH_5_tb_occur[,colSums(MOCH_5_tb_occur) > 0])
## [1] 0
Prasinophyceae_clade_VII_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Prasinophyceae_clade-VII"),]
Prasinophyceae_clade_VII_tb_occur <- Prasinophyceae_clade_VII_tb[,1:43]
length(Prasinophyceae_clade_VII_tb_occur[,colSums(Prasinophyceae_clade_VII_tb_occur) > 0])
## [1] 0
Prasinophyceae_clade_IX_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Prasinophyceae_clade-IX"),]
Prasinophyceae_clade_IX_tb_occur <- Prasinophyceae_clade_IX_tb[,1:43]
length(Prasinophyceae_clade_IX_tb_occur[,colSums(Prasinophyceae_clade_IX_tb_occur) > 0])
## [1] 0
Pyramimonadaceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Pyramimonadaceae"),]
Pyramimonadaceae_tb_occur <- Pyramimonadaceae_tb[,1:43]
length(Pyramimonadaceae_tb_occur[,colSums(Pyramimonadaceae_tb_occur) > 0])
## [1] 11
other_plastids_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "other_plastids"),]
other_plastids_tb_occur <- other_plastids_tb[,1:43]
length(other_plastids_tb_occur[,colSums(other_plastids_tb_occur) > 0])
## [1] 29
## [1] 43
## [1] 43
##                      reads_per_class OTUs_per_class
## Bacillariophyceae               1777            168
## Bolidophyceae                    312              7
## Chlorarachniophyceae              33              5
## Chlorodendrophyceae                2              2
## Chlorophyceae                      2              2
##                      reads_per_class OTUs_per_class samples_per_class
## Prymnesiophyceae               55897             50                43
## Mamiellophyceae                32273             15                31
## Pelagophyceae                  11504             10                43
## Cryptophyceae                   3872             28                31
## Dictyochophyceae                2954              7                43
## other_Prasinophyceae            2694             26                41
## Bacillariophyceae               1777            168                39
## Bolidophyceae                    312              7                34
## Rappemonads                      249              4                37
## Pyramimonadaceae                 147              7                11
## other_plastids                    93             28                29
## Chlorarachniophyceae              33              5                 8
## Dinophyceae                       25              6                11
## Eustigmatophyceae                 25              2                 9
## Pinguiophyceae                     3              1                 3
## Chlorodendrophyceae                2              2                 2
## Chlorophyceae                      2              2                 2
## Phaeophyceae                       2              2                 2
## Pavlovophyceae                     2              1                 2
## Trebouxiophyceae                   1              1                 1
##                      reads_per_class OTUs_per_class samples_per_class
## Prymnesiophyceae               55897             50                43
## Mamiellophyceae                32273             15                31
## Pelagophyceae                  11504             10                43
## Cryptophyceae                   3872             28                31
## Dictyochophyceae                2954              7                43
## other_Prasinophyceae            2694             26                41
## Bacillariophyceae               1777            168                39
## Bolidophyceae                    312              7                34
## Rappemonads                      249              4                37
## Pyramimonadaceae                 147              7                11
## Chlorarachniophyceae              33              5                 8
## Dinophyceae                       25              6                11
## Eustigmatophyceae                 25              2                 9
## Pinguiophyceae                     3              1                 3
## Chlorodendrophyceae                2              2                 2
## Chlorophyceae                      2              2                 2
## Phaeophyceae                       2              2                 2
## Pavlovophyceae                     2              1                 2
## Trebouxiophyceae                   1              1                 1
##                reads_per_class OTUs_per_class
## Cyanobacteria           400768            364
## other_bacteria         3171424          23955
## NA                          NA             NA
## NA.1                        NA             NA
## NA.2                        NA             NA



OTUs per class vs. samples in which they occur - PROTISTS vs. CYANOBACTERIA [PLOT DESCRIPTION]

##   reads_per_class    OTUs_per_class samples_per_class 
##           100.000           100.000          1013.953
##                      reads_per_class OTUs_per_class samples_per_class
## Prymnesiophyceae        1.090584e+01      7.0621469        100.000000
## Mamiellophyceae         6.296655e+00      2.1186441         72.093023
## Pelagophyceae           2.244499e+00      1.4124294        100.000000
## Cryptophyceae           7.554503e-01      3.9548023         72.093023
## Dictyochophyceae        5.763430e-01      0.9887006        100.000000
## other_Prasinophyceae    5.256155e-01      3.6723164         95.348837
## Bacillariophyceae       3.467033e-01     23.7288136         90.697674
## Bolidophyceae           6.087306e-02      0.9887006         79.069767
## Rappemonads             4.858138e-02      0.5649718         86.046512
## Pyramimonadaceae        2.868058e-02      0.9887006         25.581395
## Chlorarachniophyceae    6.438497e-03      0.7062147         18.604651
## Dinophyceae             4.877649e-03      0.8474576         25.581395
## Eustigmatophyceae       4.877649e-03      0.2824859         20.930233
## Pinguiophyceae          5.853179e-04      0.1412429          6.976744
## Chlorodendrophyceae     3.902119e-04      0.2824859          4.651163
## Chlorophyceae           3.902119e-04      0.2824859          4.651163
## Phaeophyceae            3.902119e-04      0.2824859          4.651163
## Pavlovophyceae          3.902119e-04      0.1412429          4.651163
## Trebouxiophyceae        1.951060e-04      0.1412429          2.325581
## Cyanobacteria           7.819223e+01     51.4124294        100.000000



Reads per class vs. OTUs per class:



Reads per class vs. samples in which they occurr: